Full run via scheduler last night from park to park and all parts executed but not as expected - THIS IS WIERD
1) Normal start - unpark...slew...focus....align...capture HA no issues
2) change filter to OIII no issues
3) Guide (@Hy) is all good at this point

4) at  correct time flip is pending - flip executes and takes the normal time based on my slew speeds
5) align happens and says complete - see first attached image - THIS IS NOT THE SAME TARGET
6) at this point there is no guiding - 00:31:44 Autoguiding aborted - which is right at the flip (good) - but no reason for it to STAY aborted - it should have resumed
7) at this point I have a few hours of unguided images in SII on an unknown patch of sky.....and THEN
(yes this is the weird part)
at 04:57 am the system decides to focus again on SII and THEN perform an align (3 iterations) - it is GOOD and back on target AND guiding kicks back in AND I am suddenly focusing on OIII
9 ) the system manages 1 final image in OIII with a flipped target properly centered and the image is in focus and well guided!

The 3 images here show the analysis window  and logs are attached - but WOW and WHY - the strange operation - funny thing is each function can operate but to suddenly align after 4 hours? 
Full run via scheduler last night from park to park and all parts executed but not as expected - THIS IS WIERD
1) Normal start - unpark...slew...focus....align...capture HA no issues
2) change filter to OIII no issues
3) Guide (@Hy) is all good at this point

4) at  correct time flip is pending - flip executes and takes the normal time based on my slew speeds
5) align happens and says complete - see first attached image - THIS IS NOT THE SAME TARGET
6) at this point there is no guiding - 00:31:44 Autoguiding aborted - which is right at the flip (good) - but no reason for it to STAY aborted - it should have resumed
7) at this point I have a few hours of unguided images in SII on an unknown patch of sky.....and THEN
(yes this is the weird part)
at 04:57 am the system decides to focus again on SII and THEN perform an align (3 iterations) - it is GOOD and back on target AND guiding kicks back in AND I am suddenly focusing on OIII
9 ) the system manages 1 final image in OIII with a flipped target properly centered and the image is in focus and well guided!

The 3 images here show the analysis window  and logs are attached - but WOW and WHY - the strange operation - funny thing is each function can operate but to suddenly align after 4 hours? 
I guess the main issues are 
1) why did align successfully align on nothing and then suddenly after 4 hours do another align and actually get the target
2) way did guide never resume after the flip/align at 12:30 am but suddenly start again at 5:00 am

Any insight would be helpful 
This is master branch build as of last Friday (sept 10) - beta 3.5.5