Basically what you got going on is I think your not getting the drivers right yet...
What happens when you supply the floppy is the drivers are loaded to the ram and then windows loads them to the hard drive and when you re-boot there not where they are suposed to be....
Heres what i would do.... Look at the board by the Sata connector and see what the sata chipset says...(Name) ...glc said Intel...I'm betting he's right...Just in-case take a gander....Now you have 2 choices re-read the manual or call tech support....
When I got my 74gig raptor I was installing a Gigabyte 7nnxp board and I had the same problem you have....I elected to call tech support and glad I did as the manual was misprinted...If you call them they will walk you thru the set-up process...thats what they are there for....
I am in no way trying to be sarcastic or mean... I am trying to help you use all the available resources I can....