ASR, NTFS and FAT32... any problems?

After a recent file corruption event that required me to
reinstall XP to resolve, I bought a 2nd 40GB HD and used
the Automated System Recovery Wizard to backup my whole
main drive and create an ASR floppy. Also scheduled
weekly backups. I now notice that while my main drive
(C shows up as FAT32, D: (which houses the ASR backup
file) shows as NTFS. Here's my question: if I ever need
to restore from D:, either manually or using the ASR
utility, should I expect any problems from the NTFS/FAT32
difference between D: and C:? I am not using any fancy
NTFS options (indexing, quotas, etc... not even sure what
those are, but read about them in WinHelp). Any advice or
reassurance from someone in the know would be GREATLY
appreciated.

Thanks.