Onboard and PCI-E Graphics shows blinking black screen on 8.1

Question

I have a homebrewed 3rd Gen Core i5 on an Intel DQ77MK motherboard which has onboard graphics. I also have an nVidia Quadro FX 3500 PCI-E graphics cards.
The Quadro has two DVI outputs connected to two monitors, I connected a third to the onboard graphics. So I have three monitors.
This worked fine with Windows 7. I go to install windows 8.1 and I turned off auto-updates and all the auto device driver junk. I installed the Intel drivers and the nVidia Drivers and three monitors working fine. I go to update to grab a package to remove
that stupid "SecureBoot isn't configured properly" watermark and I reboot to black screens with a cursor and nothing else. I reboot to the BIOS and turn off the integrated graphics and I can get back in - but I really want my triple monitors. 

Answer 1

black screens with a cursor and nothing else. 
So, if there is a cursor, it's not really "black", just blank.  But to be really clear "cursor" means an underscore at the top of the screen, or something else?  I have seen the former myself but don't really know what it means.  Also it has
only happened occasionally and I can't remember whether it shows on both of my monitors when it happens?  I think that when I have seen that I have had to unplug some other USB devices to get past that symptom.  E.g. my usual tricks with Win-P or
Ctrl-Alt-Delete or Shift-F10 etc. did nothing--no beeps and no drive light activity.
A reason that it could be important to know if the underscore appears on all monitors is that sometimes the boot seems to get confused about which monitor is primary, so if both monitors have different attributes (as mine do) then perhaps the symptom
could be understood as the wrong monitor getting the controls that were meant for another? 
reboot to the BIOS and turn off the integrated graphics and I can get back in 
That sounds like a driver problem but I don't know for which component, e.g. WinPE? Boot Manager?  OS?  So instead of doing that have you tried using the Advanced Boot Option to use low resolution video (AKA VGA mode)?  The BCD allows even
other video related settings.  While you are having problems it would be a good idea to turn on the Boot menu prompt, even if you don't have multiple partitions to boot, just to make it easier to use those options.  FWIW a surprise for me when I
tried this is that we are not restricted to what drivers the OS can use later.  E.g. I just used Win-P once in the OS and could make everything work normally after that.
Another thing that you could try is tracing your boot activity with xbootmgr and then finding out what is different for your two cases.
Good luck
Robert Aldwinckle