No. Unless there are differences in this regard between Windows 2000 and
XP, FAT32 won't help. On this Windows 2000/FAT32 computer, F-Prot for
DOS will not scan all files. In fact, the number of files it claims to
have scanned is considerably inferior to the number of files it scans
under Windows 98 on the same computer. Scary.
Though F-Prot for DOS is still useful for minimalist usage. If you can't
stand the pungent stench of bloat that modern Windows AV programs give
off, then you can use it to manually scan incoming files. It will do
that just fine.
As far as I am concerned, despite its limitations, I still find the DOS
version far more useful than the unhandy, clumsy native Windows scanners.