I kind of had this problem before, and I still do, only less frequently. If the xbox was warm everything would work fine, but on cold boots all I could get is xenium OS and original bios, and would frag on picking any other bios.
I think my problem is a lose connection somewhere, but I'm not sure where. It seems like I can fix the problem sometimes by lightly shaking my xbox, or just lifting it up and setting it back down lightly. I think my chip slowly pushes itself out of the pins on the pinheader.
I could also fix it sometimes by running an original xbox game w/ the original bios, then rebooting. So I'm not sure if the movement of the disc drive spinning helps cause the chip to slip back into place, or if running an original game fixes some kinda software conflict somehow.
In either case I can get my box to boot within a minute usually, but it is still damn annoying.