Thanks all for your suggestions. I do have fast boot enabled (and probably MRC cache too). I will try to disable that.
Main issue was that we have had a unit not boot up at all and a unit not boot up properly (as in Windows logo would fade in and out but stay in that state without progressing).
Both issues were fixed by writing the same bios (using a programmer or if the system would boot) or flashrom. This write should however remove anything written by the system on first boot. This makes me think that the cache or whatever else is writing to the flash chip is causing the system to fail.
I will test and update once I know if it was the MRC writing to the flash. Regards, Naveed