I am having the same problem too where the multi-aperture function will stop after the first file; the measurement table only has one entre. My files are on an external hard drive that are not backed up with a service like One Drive. I'd try I am using windows 10 and version 5.03.02 of AIJ. I've tried creating a test folder with a couple of files right on the portion of my C drive that is not backed up by external backup and still have the problem. All of my images are plate solved.
I sometimes am able to get all files to be processed after the multi-aperture tool, but usually it only processes the first slice in a stack. From time to time, I get an error that says something like "Waited 0.0 seconds before closing MP panels." Sometimes doing the Fresh Restart, restarting AIJ, or restarting the computer works. I can't quite figure out the set of conditions that work to get all files processed.
I'd appreciate any guidance you have.
Thanks,
Justus
Here is a screen shot of the setting I use on the multi-aperture photometry tool. All of my images are plate solved.