A file larger than 4GB cannot be created on a FAT32 file system, so since pretty much any backup these days is likely to be larger than this, I wouldn't be surprised if a FAT32 partition is ignored. If it's now empty, you could try deleting the FAT32 partition and creating one NTFS.
Edit: When you say "wiped", what did you do, reformat? You didn't just delete the FAT32 partition and leave unallocated space did you?
Edited by Platypus, 22 December 2012 - 01:01 AM.