I don't have an answer for you on that. I have a somewhat similar issue where I have added Emulators to MA and every time I reboot the computer, my preferences reset to the default settings and I have to re-config the new emulators. It's annoying. I have an X-Gaming unit that runs MA on it. I reached out to the company and this is what I was told to do:
"There is a batch file that re-writes the default.ini file on boot to keep the PC from ever not starting correctly due to it getting corrupted. You could just edit it to not do that if you know how, it's the startup.bat file found in the Max 2.10 folder.
Alternatively, this update would change how that works:
Instructions: X-Arcade Cabinet Software Upgrade - New Features"
I am going to try the update first and see how that goes.
I have no idea if that default.ini file is helpful to your issue or not, but thought I'd let you know
Good luck with your issue.