@Traveler
Try going into the bios --> boot --> hard disk drives here you can select which hdd is number 1, which is 2 and which is 3. This is just a hunch and may not be what your after at all.

If this doesn't work you could try changing the sata mode from ide to ahci. AHCI enables extra sata features such as NCQ, hot swap etc.
If you have XP follow this guide http://forums.pcper.com/showthread.php?t=444831
If your on vista then follow this http://support.microsoft.com/kb/922976

After you follow the steps in the link you then install intel matrix storage manager and reboot and your good to go. I've already performed this on my rig and it worked fine so i know it works.

The reason changing from IDE to AHCI would fix your problem is that the master/slave naming is from IDE, when you change to AHCI it simply says HDD 1, 2 etc.