There is no problem with using FAT32, for certan reasons, it might be even the better choice than NTFS. That said, if the partition size will be larger than 32GB, it is a must to use NTFS. Using FAT32 may cause file corruption and even loss of data hence the problem you are having.

You could use a 3rd party utility to recover the data or slave this drive to a working Windows 2000(with minimum SP3) or Windows XP(with minimum SP1) and try to access and copy the data.

If none of the above helps then from the link above, try a free partioning tool to re-size the existing FAT32 partition to 32GB or less. Another possibility would be to convert that partition to NTFS which should resolve the issue.

~TL