Dual Boot Problem

[doncolt]

OK, I'm totally lost on this one. First build and I'm waaay over my head here.
Here we go-- Asus P4R800-V Deluxe, 200gig Seagate as C:, Vantec EZ Swap as E: with two 80gig Seagates in racks. All Sata, and this is where I get lost. I've done this on IDE drives and it worked great.
Plan was to boot to E to testdrive shareware, freeware etc., keeping C clean as possible from ads and viruses. If Program is a keeper, move to C, backup C to 2nd 80 gigger in E: no os needed on E2, got it?
Installed Win Media Center 2005 on C:
Formatted E1 with DrDos, setup recognized E, finally, installed WinMCE on E. Whoopie! Got new dual boot screen, AND... shows Hardware conflict..
Now, it will not boot on either option if E1 is in the slot. boots slot empty or E2 installed fine. Here's my question:
Why would installing windows on one hard drive in E cause a hardware conflict error that goes away with the OS?
On the dual boot screen, the first OS pick always returns the error, (I'm guessing that looking for E1's OS) whatever is in E or empty.
The second pick boots to C with no E empty, C showing E with E2 installed, that all seems good. Errors out if E1 in the slot.
Repair? Reinstall? Shuffle the DMQ's and IRA's?? Oh, both E1 & E2 hard drives work fine installed as a Raid before the 200 gigger (thanx to glc!).

Thanx in advance!!! If I left anything out, lemme know.