Can a motherboard mess up boot sector of hard drive?

I have a server with a TYAN S2875ANRF with dual 1.8 GHz AMD Opteron processor 244 with 2 GB of RAM and 2 80 GB WD800 hard drives on RAID 1. The motherboard has SIl3114 RAID controller built in. I am running windows server 2003 with IIS and a couple random services, nothing extreme.

Here is what happened: The server restarted all of a sudden one day so I rebooted it and then it happened again except it displayed a blue screen first saying "machine hardware error" or something to that effect. I did a search on it and found that to mean that the processor is usually bad or the motherboard. I took out CPU2 and it ran fine for a day. Then I put CPU1 into the CPU2 socket and it would not boot. I also put CPU2 into socket1 and it booted fine again. So I assumed that socket2 must be bad on the motherboard. I kept the server running on one processor in socket1 for a while afterward waiting for a replacement motherboard and then one day I got another blue screen different from the first one and I was unable to boot after this. After restoring some hive files on the server hard drive in another system I got it working again, but I am afraid to put the hard drives back into the old server now. Is it possible that something could have written to the boot sector of the hard drive to mess it up?

I have tested the memory with memtest86 and it passed. I measured the voltage on the CMOS and it was at exactly 3 V as it should be. I have not thoroughly tested the power supply with a volt meter, but I have assumed that it was not the culprit.

I hope someone has an explanation for this. Sometimes hardware problems can be quite difficult to diagnose.

Thanks