Emulators corrupt FAT32 / BootMii

Hey everyone, this has happened to me a couple of times now. I run version 4.2U and use an external hard drive (1 TB)with 3 partitions (first one is the FAT32 then the WFBS to store games and the last I just use as an HDD) every once in awhile I will play the NES or SNES emulators through homebrew. When I try to save a state it freezes and says the root directories could not be found and then everything in the FAT32 gets renamed to something similar to that of wingdings in Microsoft word. The USB loader works just fine just that the theme and images get corrupted since it is on the FAT32. I normally just delete the files and reload them all back on.
I was just wondering if there was another solution to prevent this or a reverse solution? Thanks.

That's weird. I'd suggest;
1. Reformat the FAT32 partition
2. Re-download latest emulator and files.
3. Try making the FAT32 partition the Primary and Active partition (may trouble the WBFS partition in USB Loader)
4. Finally, try another HDD to make sure its not a capability issue.

Just a tip: you don't need a WBFS partition. Some WBFS managers (I use Wii Backup Manager myself) will save .wbfs files to FAT or NTFS. The latter has the advantage of being more easily recovered and supporting files larger than 4GB--the downside being its being proprietary. The first won't take files larger than 4GB, but WBFS managers can split images and most loaders don't have a problem with this.