Problem with drive letters in Windows NT

[gadi_sam]

I have a computer running Windows NT, with 2 physical disks, each with 2 partitions. The partitions on the primary disk are C: (master) and D: (slave), the partitions on the secondary disk are E: (master) and F: (slave). (I know that this is not the Windows’ default configuration, but that how it is).
The problem is: When I turn the computer on after it has been shut down for several months, Windows starts up with the drive letters changed to the Windows’ default (C: and E: on the primary disk, D: and F: on the secondary). This of course renders my applications inoperable. At first I thought it’s a battery problem, but I checked the battery and its voltage is OK.
The question is NOT how to solve the problem AFTER it happens (this is easy, change the drive letters using the Disk Administrator). The real questions are:
1. Why does it happen?
2. How can I PREVENT it from happening?
3. Can I somehow use one of the INI files to force MY configuration when Windows starts up? Is there a BAT file that can do the job?

[EzyStvy]

If all partitions except C were set to extended partitions instead of primary partitions they might stay the same. Not sure you can do this without data loss.

[gadi_sam]

I don't think you're right. If I can change the drive letters via the Disk Administrator tool without any data loss, then I can surely do it with a batch file or via boot.ini or some other ini file.

[Panama Red]

Not sure but this info may help.

[gadi_sam]

This info is good to know, but it doesn't help me... sorry.