There are a few things to check here -
power supply - wattage, ATX version, connections to graphics card
which version of bios do you have currently?
what is the memory situation?
when you mention the two screen boot, are the symptoms the same when using only the onboard graphics?
I would test that by re-flashing the latest bios and using only the onboard as if it appears when using your Gigabyte card then it may be all related
latest bios here -
To disable the ME Prompt, there is an option in the BIOS.
See my previous Post. Download the PDF file
Isit said that there is a new BIOS Version 0092, try it as well.
Hope this helps a bit.
I am using a Corsair HX520W power supply + latest bios in May 09 when this blank screen happens. I am 100% sure it is the motherboard that sometimes fail to detect my GTS 250 graphics card because there is one time I restart my PC and thereafter the whole screen turn blank but Window still boot up. I plug the blue VGA cable to my motherboard and true to what I suspect, there is image from my onboard VGA but not from my GTS 250 connected to monitor with DVI.
Disable the ME Prompt will also show a garbled screen on top portion occupy about 1/5 the screen and Intel admitted that the old BIOS 0069 shows a even worst garbled screen and I suspect they fix it partially only. The only way to completely by pass the split second ME screen and garbled svcreen is to disable ME completely using ctr+P but I will not be able to see the temperature and all the rest of the readings. Talk about poor implementation of such feature. They should integrate the full set of ME options into the bios.
I also encounter fan issue since you mention it. Disable ME quiet option result in a full fan speed but we lost all the motherboard monitoring information like temperature etc. The new bios also cause the REAR fan speed to slow down a lot which is no good. I think the CPU fan speed also slows down slightly. Can Intel please increase the speed for all the fans like the rear, front cpu etc.