That pause is normal. as is the "Performing Serialize". You can see that pattern other places in your logs:
[6/9/2016 4:12:46 AM] [DEBUG] [Camera Thread] Cannot set readout speed, not supported by camera...
[6/9/2016 4:13:17 AM] [DEBUG] [Main Thread] PopulateDataModel: Transferring view to the data model...
[6/9/2016 4:13:17 AM] [DEBUG] [MF Update Thread] Performing serialize...
[6/9/2016 4:32:46 AM] [DEBUG] [Sequence Thread] TEMP - Current Event15: 0
[6/9/2016 4:32:46 AM] [DEBUG] [Sequence Thread] Waking from exposure time sleep period...
[6/9/2016 4:32:46 AM] [DEBUG] [Sequence Thread] Checking to see if the CCD has a temp...[6/9/2016 3:32:05 AM] [DEBUG] [Camera Thread] Cannot set readout speed, not supported by camera...
[6/9/2016 3:32:53 AM] [DEBUG] [Main Thread] PopulateDataModel: Transferring view to the data model...
[6/9/2016 3:32:53 AM] [DEBUG] [MF Update Thread] Performing serialize...
[6/9/2016 3:52:05 AM] [DEBUG] [Sequence Thread] TEMP - Current Event15: 0
[6/9/2016 3:52:05 AM] [DEBUG] [Sequence Thread] Waking from exposure time sleep period...
[6/9/2016 3:52:05 AM] [DEBUG] [Sequence Thread] Checking to see if the CCD has a temp...What appears to happen is that something goes bad with the telescope connection and causes a frame restart
`[6/9/2016 5:08:31 AM] [DEBUG] [CP Update Thread] ASCOM Telescope: Error in GetLst : Timed out waiting for received data
......
[6/9/2016 5:12:32 AM] [DEBUG] [PHD2 Listener Thread] Error: Guide star reported as lost!
[6/9/2016 5:12:32 AM] [DEBUG] [PHD2 Listener Thread] Adding sequence level notification: Guide star lost!
[6/9/2016 5:12:33 AM] [DEBUG] [Guider Camera Thread] Frame restart: Guide star was lost.
[6/9/2016 5:12:33 AM] [DEBUG] [Sequence Thread] ASCOM Camera: Attempting to abort exposure...
[6/9/2016 5:12:33 AM] [DEBUG] [Sequence Thread] ASCOM Camera: Exposure aborted...
[6/9/2016 5:12:33 AM] [DEBUG] [Sequence Thread] ASCOM Camera: Blocking until image is aborted...
[6/9/2016 5:12:33 AM] [DEBUG] [Camera Thread] ASCOM Camera: external abort...
[6/9/2016 5:12:33 AM] [DEBUG] [Camera Thread] SGM_CAMERA_CAPTURE complete...
[6/9/2016 5:12:34 AM] [DEBUG] [Sequence Thread] ASCOM Camera: Image is aborted...
[6/9/2016 5:12:34 AM] [DEBUG] [Sequence Thread] Adding sequence level notification: Frame restart: Guide star was lost.`
Not sure what caused the telescope error. Appears to have been temporary.
Thanks,
Jared