I've put together a system for myself and one for a friend:
p4 3.0 on gigabyte
amd 64 3000+ on msi k8t neo
Both originally had 80gig wd 7200 rpm harddrives with xp loaded as the os and both worked fine. But then we thought why not get a raptor 36 10000x each and spice things up a bit and so we had to format both and install the os on the faster raptor. When I boot with just the raptor connected I'm good. I can plug the 80 in while windows is loaded and access the partitions on both drives. But when I try to boot with both drives plugged in (sata) I originally got a message on boot saying NTLDR missing and it hangs. I figured it was something to do with both drives at one point being used for boot drives so I used this lifeboat utility from wd to reformat and repartition the 80's as secondary storage. Now on boot I get "error loading os". With hesitation I flashed the bios on the k8t neo with no luck. What have I done!?
Your problem is caused by a little knowledge. That's a dangerous thing. The root partition on both drives is set 'Active' for booting, a sure recipe for disaster. The machine can't figure out which one to boot from.
I'm not sure that the partition on the 80 gig can be set as inactive without a repartition, but owning a copy of PowerQuest Partition Magic or some such partition manager would be a plus. Especially if you intend to keep messing around in the future.
The problem now is that the boot.ini file on the Raptor is set, I bet, to look to the 80 gig drive as the boot partition. Use Notepad to ssorrect that.