Problem with HD on raid controller

I have the abit kg7-raid mobo. I have 2 harddrives, a 27GB 5400rpm Maxtor, and a 100GB 7200rpm Wester Digital. They aren't in a raid config, but are connected through the raid controler. One is the master of eide 3 and the other is the master of eide 4. Ok, for a while everything went fine. Except that once in a while I'd get the message at startup that windows could not start because of a hardware configuration problem, but I could shut off the powersupply, then restart and it would work. But then I'd start getting the message at startup "Windows could not start because of the following file is missing or corrupt: \windows\system32\config\system You can attempt to repair this file by starting...." I boot with the windows xp cd-rom, and at the repair screen, I run chkdsk /r /p, this usually fixes the file, and I can startup, for a while. But it happens again and again more frequently until windows won't startup at all, no matter what I do. Then I have to format and reinstall windows, which will start working for another few weeks. Any ideas?

Rest of my system

Abit KG7 RAID
1.8 Athlon XP
512 PC2100 Ram (crucial)
windows xp