The log you sent never attempted to flip so that could be what your seeing? It starts on the east until 23:27, then a new sequence is started at 23:28 and the mount is on the west. So... not sure I can help since SGPro never even attempts to start a flip:
[9/20/2016 10:04:48 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:04:48 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:06:03 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:06:03 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:07:21 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:07:21 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:08:39 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:08:39 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:09:57 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:09:57 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:11:15 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:11:15 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:12:37 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:12:37 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:13:55 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:13:55 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:15:50 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:15:50 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:17:08 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:17:08 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:18:30 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:18:30 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:19:48 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:19:48 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:21:06 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:21:06 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:22:28 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:22:28 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:23:46 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:23:46 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:25:39 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:25:39 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:25:49 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:25:49 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:26:38 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:26:38 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:28:20 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:28:20 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side
[
[9/20/2016 10:28:31 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:28:31 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:30:37 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:30:37 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:31:10 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:31:10 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:32:57 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:32:57 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:33:08 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:33:08 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:34:08 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:34:08 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:35:28 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:35:28 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:36:50 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:36:50 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:37:01 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:37:01 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:46:35 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:46:35 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:46:46 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:46:46 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:48:03 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:48:03 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:49:21 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:49:21 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:49:31 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:49:31 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:50:56 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:50:56 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:51:12 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:51:12 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:52:56 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:52:56 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:54:36 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:54:36 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:55:03 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:55:03 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:56:38 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:56:38 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:57:36 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:57:36 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 10:58:57 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 10:58:57 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:00:15 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:00:15 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:01:36 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:01:36 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:01:46 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:01:46 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:03:31 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:03:31 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:03:49 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:03:49 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:05:16 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:05:16 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:06:07 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:06:07 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:07:42 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:07:42 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:08:07 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:08:07 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:09:42 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:09:42 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:11:01 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:11:01 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:12:36 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:12:36 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:13:54 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:13:54 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:14:40 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:14:40 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:16:01 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:16:01 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:17:23 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:17:23 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:18:17 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:18:17 PM] [DEBUG] [Sequence Thread] Meridian flip not needed, telescope on East side[9/20/2016 11:28:27 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:28:27 PM] [DEBUG] [Sequence Thread] Telescope is on the West side of the mount
[9/20/2016 11:28:27 PM] [DEBUG] [Sequence Thread] Meridian Flip not needed, Hour Angle < Degrees Past To Flip: -177.692424621745 < 0[9/20/2016 11:28:36 PM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/20/2016 11:28:36 PM] [DEBUG] [Sequence Thread] Telescope is on the West side of the mount
[9/20/2016 11:28:36 PM] [DEBUG] [Sequence Thread] Meridian Flip not needed, Hour Angle < Degrees Past To Flip: -177.651393765772 < 0[9/21/2016 4:46:26 AM] [DEBUG] [Sequence Thread] Checking if Meridian Flip is needed
[9/21/2016 4:46:26 AM] [DEBUG] [Sequence Thread] Telescope is on the West side of the mount
[9/21/2016 4:46:26 AM] [DEBUG] [Sequence Thread] Meridian Flip not needed, Hour Angle < Degrees Past To Flip: -97.8378212670473 < 0