Copying relevant bits from the log file here:
Note that around 10:01:56 is when it finishes capturing the frame for auto center after the flip. And then I wait for a minute or so before aborting.
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] Telescope is on the West side of the mount
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] Meridian Flip needed, Hour Angle >= Degrees Past To Flip: 0.75330732285634 >= -0.25
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] Running blocking meridian flip...
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] Handling monitoring event (Good Night System, Status): (Crescent Nebula) Running automatic pier flip...
[9/10/2016 10:00:22 PM] [DEBUG] [Sequence Thread] GNS: Sent status message to GNS ((Crescent Nebula) Running automatic pier flip...)...
[9/10/2016 10:00:22 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Starting Meridian Flip Procedure
[9/10/2016 10:00:22 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Calling SGM_TELESCOPE_SOLVE
[9/10/2016 10:00:22 PM] [DEBUG] [Pier Flip Thread] Meridian flip: Waiting for scope solve to complete...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] SGM_TELESCOPE_SOLVE message received...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Telescope solve with plate solver PlateSolve2...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Setting filter for scope sync...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Setting filter position 4...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Filter position 4 is already set. Skipping...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Plate solving scope frame...
[9/10/2016 10:00:22 PM] [DEBUG] [Telescope Thread] Created full file name (file does not exist): C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\plate_solve_image.fit
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] SGM_CAMERA_PLATE_SOLVER_CAPTURE message received...
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] Alnitak Flat Box - Getting shutter status
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] Alnitak Flat Box - Updating Device Variables - Model: 99 Motor Status: 0 Light Status: 0
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] Collecting FITs headers for plate solve frame...
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] Collecting FITs headers for plate solve frame...
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] ASCOM (QSI) Camera: setting gain to LOW...
[9/10/2016 10:00:22 PM] [DEBUG] [Camera Thread] ASCOM (QSI) camera: setting normal speed readout...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] QSI expose and download: 16.3500035s
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] Created full file name (file does not exist): C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\plate_solve_image.fit
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Locking bitmap for disk write...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Opening file stream...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Writing FITS headers...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Traversing and persisting bitmap data...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: FITS block fill...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Unlocking bitmap...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Closing file stream
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] Internal Interface: Set Preview...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] Display image preview using asynch task...
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] =========== Save file took 124 ms
[9/10/2016 10:00:39 PM] [DEBUG] [Camera Thread] SGM_CAMERA_PLATE_SOLVER_CAPTURE complete...
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] FitsFileHeaderData: Angle - 0
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] FitsFileHeaderData: Scale - 0
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] FitsFileHeaderData: RA - 20.1979342031878
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] FitsFileHeaderData: DEC - 38.4810309708516
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: RA (HRS) - 20.1979296023183
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: RA (RAD) - 5.28780560469726
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: DEC (DEG) - 38.481030743139
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: DEC (RAD) - 0.671620686028936
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: SCALE - 7.6483
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: Width - 831
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: Height - 626
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSove2 Param: Regions - 999
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] PlateSolve2 Command Line:
[9/10/2016 10:00:39 PM] [DEBUG] [Telescope Thread] C:\Users\manoj\AppData\Local\SequenceGenerator\PlateSolve2.exe 5.28780560469726,0.67162068602894,0.03081348396578,0.02321208298746,999,C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\psXSolve_2.fit
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Plate solving scope frame successful, scope is synced, writing FITs header info...
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Checking to see if solve might be bad...
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Solve appears to be good...
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Telescope: Syncing to J2000 RA: 20.1976295072802 Dec: 38.4756698045752
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Telescope Sync: Passed in J2000 but mount requires JNOW, converting...
[9/10/2016 10:00:41 PM] [DEBUG] [Telescope Thread] Telescope: Syncing to JNOW RA: 20.2080735738452 Dec: 38.5320410767573
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Attempting to write fits header info for C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\plate_solve_image.fit
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Opening fits file...
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Successfully opened fits file...
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Writing fits headers...
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Closing fits file
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Syncing the rotator to 40.46 degrees...
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] ASCOM Rotator: Sync complete. Camera angle is 40.46; Reported pos rotator position: 359.93
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] Scope solve complete...
[9/10/2016 10:00:46 PM] [DEBUG] [Telescope Thread] SGM_TELESCOPE_SOLVE message complete...
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Meridian flip: Scope solve complete...
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Solve and Sync was Successful
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Stopping the Auto Guider
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Attempting to stop PHD2 guiding...
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Checking PHD2 state...
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Pre-Wait : Guiding
[9/10/2016 10:00:46 PM] [DEBUG] [Pier Flip Thread] Sending to PHD2:
{"method": "get_app_state", "id": 1001}
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Post-Wait: Guiding
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] Sending to PHD2:
{"method": "stop_capture", "id": 1004}
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] Checking PHD2 state...
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Pre-Wait : Guiding
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] Sending to PHD2:
{"method": "get_app_state", "id": 1001}
[9/10/2016 10:00:47 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Post-Wait: Guiding
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] Checking PHD2 state...
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Pre-Wait : Guiding
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] Sending to PHD2:
{"method": "get_app_state", "id": 1001}
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] PHD2 GetPhdStatus - Post-Wait: Stopped
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] PHD2: Successfully stopeed PHD2...
[9/10/2016 10:00:48 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Sending Telescope command to execute meridian flip
[9/10/2016 10:00:48 PM] [DEBUG] [Telescope Thread] ASCOM Telescope: Pier side is West
[9/10/2016 10:00:48 PM] [DEBUG] [Telescope Thread] ASCOM Telescope: attempting pier flip using sideOfPier
[9/10/2016 10:00:48 PM] [DEBUG] [Telescope Thread] Setting Pier East
[9/10/2016 10:01:16 PM] [DEBUG] [Main Thread] PopulateDataModel: Transferring view to the data model...
[9/10/2016 10:01:16 PM] [DEBUG] [MF Update Thread] Performing serialize...
[9/10/2016 10:01:38 PM] [DEBUG] [Telescope Thread] ASCOM Telescope: Pier side is East
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Telescope command to meridian flip has completed
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Adjusting rotator for flip...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Sequence is running, querying running target for target rotation info...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Attempting to resolve camera angle...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Syncing rotator to post flip sky angle: 220.459991455078...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Syncing the rotator to 220.46 degrees...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] ASCOM Rotator: Sync complete. Camera angle is 220.46; Reported pos rotator position: 359.93
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Camera already adjusted to 220, continuing...
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Telescope has performed meridian flip
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Flipping Auto Guider calibration data
[9/10/2016 10:01:38 PM] [DEBUG] [Pier Flip Thread] Sending to PHD2:
{"method": "flip_calibration", "id": 1005}
[9/10/2016 10:01:39 PM] [DEBUG] [Pier Flip Thread] Autoguider (PHDv2) successfully flipped calibration data
[9/10/2016 10:01:39 PM] [DEBUG] [Pier Flip Thread] Meridian Flip: Performing Auto Center
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Center telescope message received...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Solving with Plate Solver PlateSolve2...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Setting filter for auto center...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Setting filter position 4...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Filter position 4 is already set. Skipping...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Performing auto center step 1...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Skipping step 1...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Auto center reference frame solved successfully...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Performing auto center step 2...
[9/10/2016 10:01:40 PM] [DEBUG] [Telescope Thread] Created full file name (file does not exist): C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\plate_solve_image.fit
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] SGM_CAMERA_PLATE_SOLVER_CAPTURE message received...
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] Alnitak Flat Box - Getting shutter status
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] Alnitak Flat Box - Updating Device Variables - Model: 99 Motor Status: 0 Light Status: 0
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] Collecting FITs headers for plate solve frame...
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] Collecting FITs headers for plate solve frame...
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] ASCOM (QSI) Camera: setting gain to LOW...
[9/10/2016 10:01:40 PM] [DEBUG] [Camera Thread] ASCOM (QSI) camera: setting normal speed readout...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] QSI expose and download: 16.387233s
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] Created full file name (file does not exist): C:\Users\manoj\AppData\Local\SequenceGenerator\Temp\plate_solve_image.fit
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Locking bitmap for disk write...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Opening file stream...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Writing FITS headers...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Traversing and persisting bitmap data...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: FITS block fill...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Unlocking bitmap...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SaveFileBmp16: Closing file stream
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] Internal Interface: Set Preview...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] Display image preview using asynch task...
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] =========== Save file took 135 ms
[9/10/2016 10:01:56 PM] [DEBUG] [Camera Thread] SGM_CAMERA_PLATE_SOLVER_CAPTURE complete...
[9/10/2016 10:02:39 PM] [DEBUG] [PHD2 Listener Thread] PHD2 - No messages received from PHD2 for 1 minute, checking socket with status...
[9/10/2016 10:02:39 PM] [DEBUG] [PHD2 Listener Thread] Checking PHD2 state...
[9/10/2016 10:02:39 PM] [DEBUG] [PHD2 Listener Thread] PHD2 GetPhdStatus - Pre-Wait : Stopped
[9/10/2016 10:02:39 PM] [DEBUG] [PHD2 Listener Thread] Sending to PHD2:
{"method": "get_app_state", "id": 1001}
[9/10/2016 10:02:39 PM] [DEBUG] [PHD2 Listener Thread] PHD2 GetPhdStatus - Post-Wait: Stopped
[9/10/2016 10:02:55 PM] [DEBUG] [Main Thread] Centering: User abort...
[9/10/2016 10:02:57 PM] [DEBUG] [Auto Center Closing Thread] Aborting auto center, waiting for centering routine to terminate...
[9/10/2016 10:02:58 PM] [DEBUG] [Telescope Thread] Aborting auto center...
[9/10/2016 10:02:58 PM] [DEBUG] [Telescope Thread] Auto center aborted, closing centering dialog...