Unable t repair disk permissions on an external FAT 32 drive

Yesterday suddenly my disk permissions on my Aperture library file changed. It's located on an external fat 32 drive. I'm unable to repair it with disk utility. Now Aperture won't run anymore until I repair this file. Are there any other options then disk utility?

DU can not repair Windows formatted drives. Need to boot into Windows and use its utilities for disk repair.
It's not a goo idea to keep Mac OS X applications or data files on a non-Mac formatted drive. FAT32's filesystem is not compatible with the Mac's. Portions of a file may be removed on the FAT32 drive and it's not fully compatible with OS X filenames and legal filename characters.

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