I haven't tried to do this sort of thing with Win7 (yet), but IIRC (at least in the XP days) Windows Setup copied the driver for the primary disk controller to a special location. If you switched the controller the boot drive was attached to, that driver had to be replaced somehow. Sorry to be so vague, but it has been years since I've dealt with this issue, and I'm not even sure it is still applicable in Win7.
The years just pass like trains. I wave, but they don't slow down.
-- Steven Wilson