To avoid corrupted saves, I highly recommend to have only one megamod installed at a time on a very cleaned PC (no laptop) and the less background applications running as possible …
SH3 Commander is not bugged at all, it’s a wonderful must have application, certainly the best ever for SH3!
Here, for testing purposes, I often save close to harbors, underwater or not, very close to convoys etc without reloading problems

But each one’s PC is always different…