Solved my problem.
Jer, this might not help you since your chip is internal. In your case I can only recommend removing all other cards from the pc, and resetting the bios to default.
My problem was that even though I have a Via 6241 card it WILL NOT flash in my PC. PERIOD. My complete pc spec is an Asus P5B-Dlx, C2D E6600, 2GB GSkill HZ DDR2-800, X1900XTX, 2 Hdds in Raid0&1 (but those are unplugged), 650W psu, Pioneer 111-L, pci wifi card, and the via card. It will NOT work.
I took the card down to an older AMD machine (1200Mhz) plugged in the via card, hooked up xbox, had a hell of a time figuring out how to can an older bios like that to detect a usb thumb drive to boot from (Usb dos compatibliy must be on, and boot from usb-fdd) then it worked first time no problems. It was simple to do.
There must be an issue in how certain PCs work with the via card. I think newer is less compatible.