This is odd, my new build will only boot when I leave the flash drive in that I used to load raid drivers during Win 7 installation. I loaded the driver after my first successful boot for the Intel RSTe RAID controller, the board is an Asus P9x79 Deluxe. The driver that I used was the latest v3.0.0 version from the Asus support website for my board.
I thought it might be something wrong with the MBR, and when i check that using the Win7 DVD to repair, then it tells me that there is no OS found.
I have (twice) booted, removed the flash drive in question, downloaded, and updated the RAID controller driver. The correct driver appears in the device manager, the drives appear to work normally, and yet when I restart I get a no bootable drive error. All I then have to do is stick the flash drive in and restart and everything loads just fine.
I am beginning to think that this is a MB error and that I need to RMA the board. I have also had a problem with the PCIe slots where it will not clear POST when the GPU is in that slot. The second slot is full speed as well so I am using that one with no problem.
I just thought of something, the ctrl + I that is supposed to get me into the RAID controller during POST, does not work. This would support the thought that the controller driver is not actually functioning until after windows loads, because the graphical Intel RSTe program works just fine.
I can confirm that this is a driver issue, I have replaced the flash drive with a spare and only copied the x64 drivers for Intel RSTe onto it and I can now get a successful boot with only that flash drive inserted.
So, now I have my flash drive back, and I have yet to see a performance loss once windows is loaded. POST takes a little longer, probably because I am using a older flash drive that is pretty slow, and this whole thing is a little weird, but it's an added layer of security...if I have that flash drive with me then no one can get my computer to turn on!