Windows won't boot! Windows protection error.

I just upgraded my mother board to a MSI and now I can't boot to Windows at all! I'm using two different versions of windows on seperate hard-disks (never at the same time) and both won't boot. I can get to Safe-mode in Win98. My system was fine before I upgraded.
System:
Motherboard - MSI, K7N2 Delta, Nvidia nForce 2 based.
CPU - AMD XP 2400+ T-bred.
CPU Cooler - 2 x 8000-rpm fans on Kanie Hedgehog (big heatsink).
Memory - Kingston 256Megs, two sticks for 512megs. (Says: Kingstort /VR, KVR266X64C25/256. I don't know much about memory.) It fits the DDR1 slot.
Graphics - Nvidia 5600.
Power supply - New, Allied brand, ATX-style, 450Watt.
OS - Windows 98, Windows XP (SP1)
(Win98 and WinXP are on seperate hard disks. Never used at the same time).
Problem:
1. When I boot to Win98 it just says "Protection Error, you will need to restart your system".
2. When I boot to WinXP it says "A problem has been detected and windows has been shut down to prevent damage to your computer."
Fixes and diagnostic:
1. Diagnostic lights on mother board cycle and and say OK.
2. I can get to Win98 Safe-Mode or Command prompt.
2. I don't have any other PCI cards installed except video.
3. I'm using only one of the memory sticks just to rule out the other (tried both).
4. I have most of the on-board peripherals disabled (sound, ethernet, serial. parallel, etc...).
5. Tried upping the voltage on memory. Same problem.
6. Tried setting memory for 100mhz. Same problem.
7. Tried reseating the memory. Same problem.
8. CPU temp is well within range at around 109F.
Questions:
What could the problem possibly be? I will try anything!
1. Is there some kind of safe mode for the hard drive settings?
2. Is there some kind of safe mode for memory speed?
3. Give me some hints! Upgrading the MB shouldn't be this hard! What am I overlooking? Thanks for any replies!

Quote
Originally posted by Falconis Progmadn
This can easily be caused by not setting the jumper pins correctly when having both of the HDDs installed on the same IDE cable.
Obviously you would have to change the jumper short every time you retry each HDD.
I am not following your line of thinking here. Win98 needs to on the primary drive, primary channel in most cases, yet XP can boot from any location, and any drive letter. So why would there be a need to constantly swap jumpers? Only thing needed is the Boot.ini file on the main drive, and it will boot from any OS listed there.

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