I can't imagine what might be causing this. Was there something in the patch that changed some underlying game fundamentals?
There are some suggestions regarding mm7che problems in this thread
Thank you immensely, Kezardin. Your link helped me solve my problem.
For anyone who encounters this problem themselves, it was a Windows 7 problem where I had to run the Editor as an Admin. I had been wondering about that, but had dismissed it since the data seemed to be writing to the save file, according to the Editor. I checked again, after I enabled Admin, and it was the in-game values the save was showing when I booted it up.
I know I should try to enjoy the M&M games without cheats, which I have in the past, but as me replaying them is primarily due to nostalgia, I feel like I just want to breeze through the game, maybe find a bit of challenge in the latter part of it, and experience the storyline.