Flex
I knew that the conversion utility that shipped with Windows 2000 always used a 512-byte cluster size but I thought that the one with XP could use other sizes. When the partition was originally formatted as FAT32 was this done by XP format?
This from Microsoft...
Cluster Alignment for NTFS vs. FAT
On NTFS volumes, clusters start at sector zero; therefore, every cluster is aligned on the cluster boundary. For example, if the cluster size was 4K and the sector size was 512 bytes, clusters will always start at a sector number that is a multiple of 4096/512 — for example, 8.
However, FAT file system data clusters are located after the BIOS Parameter Blocks (BPB), reserved sectors, and two FAT structures. FAT formatting cannot guarantee that data clusters are aligned on a cluster boundary.
In Windows 2000, CONVERT handled this problem by forcing an NTFS cluster size of 512 bytes, which resulted in reduced performance and increased disk fragmentation. In Windows XP, CONVERT chooses the best cluster size (4K is the ideal).
To maximize NTFS performance, Windows XP FORMAT and the new OFORMAT tool format a new file system as FAT or FAT32, ensuring that the data clusters are aligned on at least a 4K boundary and that the FAT32 cluster size is 4K or larger.
Anyway, give the position you're in now I think you'll probably need to reformat.
More information here