After flashing a new bios it is good procedure to clear the bios, apply default settings, and reapply any changes you have done in the past. I suggest you do this before trying a repair install.
Do you use raid or not? If not this should be disabled in bios. If raid is not being used you do not need a raid driver and there would be no Yellow question mark. If raid is being used the question mark means that the driver has improperly loaded. I've never used raid devices so check here at Anandtech or use google for the procedure to reload faulty raid drivers. Generally devices can be removed in device manager and redetected upon bootup, but I'm not sure if this applies to raid drivers.
Try these before trying the repair install.
Jim