Hello Beaver, welcome to PCHF.
Well, first of all, the MSI x48 Platinum motherboard, believe it or not is not Vista compatible. At least, not until you install the latest BIOS update for this board. You should be running version 2.0 or above:
MSI -- MICRO-STAR INT'L CO., LTD.
Not sure what effect having a previous version of the BIOS will have altogether, or if it is the direct cause to your issues, but I do know that version 2.0 includes Vista support for eSATA and onboard Audio.
The only other thing I can think of that could cause Setup to freeze is the CD itself. Make sure that the CD is clean and unscratched... and original!
Finally, make sure that Setup is actually frozen by tapping the [Num Lock] key. I always use the number lock key to determine if a PC has really crashed or not. If you can enable/disable the number lock key, then it has not crashed, so it may be a good idea to leave the PC for an extra hour or so to do it's thing!!
EDIT: Marked as Answered.
