Glad that worked for you!
Back to your save issue:
It was again an issue with how unity reports play mode and transition of play mode. I used the improper way and while your
OnApplicationQuit is called, the flag was already showing false, which made the
GlobalVariables to return their editor values instead of their still valid runtime values.
I fixed that and some other cleanup issues regarding those events and now you should have access to the correct Global Variables values inside
OnApplicationQuit.
Now i don't want to release that version to everyone with those changes without further testing, but i also don't want you to wait too long. So if you feel comfortable using a pre-release i built a version with that fix(and some other changes) and you can test for yourself if my changes fixed the problem for you. But keep in mind its a pre-release, so make a backup if necessary and you probably don't want to ship your project until you can use the release version of the plugin.
You can find this pre-release
here, or you can wait until i fixed some remaining issues and managed to test those changes further.
Best regards
Nico