HDD Mystery

I got two HDDs, one has 160GBs and the other 250GBs. Both are bi-partitioned (50-50) and for some reason, Windows 2000 ordered them as follow:

Disk1_Vol1 as C
Disk2_Vol1 as D
Disk1_Vol2 as E
Disk2_Vol2 as F

Drive E holds the Windows 2000 system files and is of NTFS format while all others are FAT32.

My problem is that Windows 2000 is screwing up Drive F; it reports the correct disc comsuption, but all files are on the root folder can't be read and all folders are empty.

If I boot the computer in Windows 98 SE mode, it doesn't even "see" Drive F.

Could this be because there's a NTFS-formatted drive before the FAT32 one? And is there a way to recover my files or there's no salvation short of formatting Drive F to NTFS (which will erase all files)?

The system has two OSs: 98SE and 2000SP4. To avoid problems with the Program Files folder, 98SE is on drive C while 2000SP4 (FAT32) is on Drive E (NTFS).

Last thing done to drive F was running diagnostic tools and executing eMule (which uses drive F as dumping folder for completed files).

Drive F has about 115GB, 27 of which are already used; of that, 7GB are files stored on the root folder (F:\). Now, these CAN be "seen" but not used (MP3 files won't play on Winamp, ZIP files accuse that the file is corrupted or damaged, AVI files won't play and so on...).

But all other folders (F:\SOMETHING, F:\BACKUP) won't show their contents.

I won't be able to test this drive on another system until Tuesday but my guess is that Windows 2000 can't "see" drive F because of "E" having a NTFS file system. I can't think of any other reason.