You could blame it on ms wanting fat32 to die with a vengance. It could be on the linux side. I'd just back up the files on a computer that you can back them up to, reformat the drive to fat32, or rather ntfs (linux is now successfully read/write compatible with ntfs). And then pull a reformat with fat32. But, you might as well format to ntfs and put your files back on there either way whichever format you decided to have. Now the only problem i see with ntfs is idk whether or not osx supports it or not, so unless your plugging your drive into an osx machine i don't really see a problem. You should test that actually, plug into an osx machine sometime and see if it has ntfs read/write support, and if it does, then you can say goodbye to all of your fat32 woes completely for a superior drive format.
But, yes, ntfs is a lot better than fat32, linux does support read/write capabilities with ntfs, so if you chose to replace fat32 with ntfs, you'd definitely get rid of all of your fat32 problems completely. On the other hand reformat that drive to fat32 and put your data back on and see if that problem persists or comes up again, then you'll definitely know for sure if you should try out ntfs on your drive.
EDIT: for ntfs read/write support your distro needs the ntfs-3g driver....it's ok, all distros have it...or at least better have it. It's as easy as trying to write to an ntfs medium in linux to show if you have the driver or not. If you don't, take a quick stroll down repository lane, grab the ntfs-3g driver, install, and configure it.