I think the reason these issues haven't been fixed yet is because the cause hasn't been pinpointed. Some peolpe have issues, others don't. I, for one, never have these issues. I save whenever, wherever and it's all good. Others stick to specific rules (no saving underwater or near contacts, for example) with mixed results.
To me, it is the most illogical and puzzling issue with SH4.
Hold on... :hmm: yes, once. RFB was generating insanely large save files. Figured out it was because of the replay data always getting saved. Ran out of discspace, so I opened up the folders with the save-games and deleted the replay data. All save-games got corrupted, even the ones I didn't mess with. (deleted the temporary replay data as well, in an effort to make it impossible for the game to save it)
I loaded a war patrol, let it finish loading till I was standing in the control room, facing my XO. Then I tried loading a save-game I hadn't messed with (but wouldn't load before) and it worked!
Maybe it can be of some use to someone in the future. :hmm: