In my opinion, based on my experience playing SH3 and the fact that i'm a software developer (like many here, probably), I'd say that this bug is triggered by long loading times, and this might be caused by a lot of factors. From scenario complexity (nearby convoys, etc.) to harddisk/filesystem speed.
Sometimes I have fixed it by "touching" the files in the save directory, sometimes I had to remove some saves, sometimes just nothing won't work and an older save will do.
I have even experienced a period where I just can't start a new campaing and load it after a few saves, and the bug was gone after some months of forgetting about the game.
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