nadassar OK, so I've been able to diagnose the cause of your problem in the bugged save. Mercifully, it isn't the F@#$ing PartySwitch bug, which means that we can perhaps be a little more confident that my fixes to the damned thing will actually suppress all known issues.
It's that switch #8 is set to on. This switch was implemented by @Lamsey to disable the major menu items during the Nyst's Battleground section of the 2nd Gathering. After making a reasonably rigorous check for code that would change that switch, I have to conclude that you must have accidentally turned it on while using the save editor.
Presuming it was RPGMakerSaveEdit.exe, the likeliest explanation is a misclick shortly after the Switches window appears. Since it's switch #8, it's always visible when the screen first loads.
As long as you're satisfied with this explanation, I'm closing the case.