Although this is only marginally on topic, I also experienced FAT corruption with Windows 3.1 when using partitions formatted as 4GB (unsigned int) rather than the standard 2GB (signed int). I believe this worked because DOS 7.1 supported this kind of formatting, although I don't recall exactly. I do believe that the corruption happened from Windows 3.1 having a problem with it though, so it's not a DOS 7.1/Windows 3.1 compatibility problem per se, but more of a compatibility side effect of a feature.

My rule of thumb now, for maximum safety, is to never install Windows 3.1 to a partition larger than 2GB, and to always use FAT and not FAT32.

I believe symptoms of the problem are visible after loading Windows 3.1, exiting back to DOS, and trying to use the DIR command. I think it throws an error.

I should have taken better notes. This is all anecdotal and from memory.