It sounds to me like your mount isn't flipping when it is supposed to for some reason, but rather hitting a stop and taking exposures stuck at the stop. I had that same result that you are talking about the other night when I forgot to setup my meridian flip at all... luckily the mount safety stops performed their role and the mount sat there patiently for me to find it in the early morning when the hairs stood up on the back of my neck and I jumped out of bed in a panic.
There are a few ways to skin the meridian flip cat but I found that putting it in the "Global Triggers" section makes it the easiest for me. As long as I stick it in there, my meridian flip settings are set correctly for my mount in the Settings > Imaging menu, and my safety stops are correctly configured on my mount... it works every time. When I try to put my meridian flip trigger anywhere else... well, it is hit or miss.
I've attached screen shots for my basic settings that I use for every imaging session in the advanced sequencer in case it helps anyone... notes below:
When I add a target to the advanced sequencer, I place all my target prep and target imaging instructions sequentially in the target's instruction box. The initial autofocus under Target Preparation is just to get everything started. All the remaining autofocus triggers are under the imaging instructions.
I put my autofocus intervals for time/temperature in the imaging trigger section. I use calculated focus offsets so I don't need to autofocus between filter changes. I put my loop condition (until astronomical dawn) in the imaging loop condition section. Then my imaging instructions instructions are generally to take a handful of subframes in each filter, and then dither once after all the filters have cycled... in the case below, it would be 2x frames each of SII, Ha, OIII, then dither, then repeat.
My closing instructions include a parallel instruction where the guiding will stop, the camera will warm, and the scope is commanded to the park position simultaneously.
Again, just offering an example of how I run it... there is more than one way to do this. But for those who are just starting out, it may offer a starting point.
Here is how I set up my meridian flips... do not use these specific settings, they will not work for you... they work for me and my setup and I have done the calculations to make it work.. notable settings that I use are "pause before meridian 0 min" because my mount can track through the meridian without hitting anything (to include safety stops... pause before meridian is for when you need your mount to stop tracking before it even hits the meridian because of collision hazard. Minutes after meridian is the soonest after the meridian passes that the flip will be directed. Max minutes after meridian is the latest the mount can continue to track past the meridian before a safety stop/pier collision occurs... calculated at 4 minutes (time) per degree of RA rotation.
So all that being said, your specific settings will have to be worked out based on your configuration, mount type, etc... but try putting the meridian flip in the global trigger area. I used too many words.
I would also backup the suggestion that you set up an imaging session during the day... set up your advanced sequencer with all the settings for a 60 minute imaging session, meridian flip, etc. Then go into your planetarium software, find a target (can be star... anything really) about 5 -10 minutes before the meridian, go to framing assistant, "get coordinates from planetarium", load image, add target to sequence... check the sequence... start the sequence and wait and watch.
Your meridian flip should happen on schedule... if not... you can troubleshoot during daytime without losing imaging time. Change settings, reimport a new target from your planetarium and try again.
