This is driving me nuts. EVERY time I boot my machine, my 4K monitor has the desktop on it at 640x480 resolution and my main 2.5K monitor is just empty desktop.
I have spent five minutes reprogramming the resolution back to 4K on the 4K monitor, reprogramming the 2.5K display to be my main and reprogramming my Wacom tablet to use the main monitor and then rearranging my desktop icons the way I want them. 
Next reboot, I'm back to VGA mode on the 4K display!!
 
Is there a driver update to fix this? I have downloaded several new drivers in the past month, but this problem is off and on again. This time after updating Winsat to fix the 32MB cache bug.
 
I've rebooted the machine several times, but the monitor resolution never comes back!

I'm not running Windows 10. Windows 7 64-bit here.
I have had this problem with several of the nVidia drivers from 347.52 to 355.60.
The system refuses to boot with my 4K monitor in anything but VGA resolution and my desktop always goes to that monitor, despite me taking the time to reconfigure everything the way it should be, at every start up. As soon as I shut down and restart, it's back to 640x480 with the desktop on the secondary 4K monitor instead of on the 2.5K primary monitor. If I shut off the 4K monitor, my desktop moves back to my primary, but my tablet can't get a cursor on that screen.
It was behaving itself for a while before I installed the patch to fix WinSAT's memory error, but after several reinstallations of the nVidia driver, I just wiped the C: drive and reinstalled the last good backup image of the drive. However, it seems that the hardware is broken, because even with a good working image of the boot drive, it's still insisting on setting the 4K monitor to VGA.
 
Maybe I can fix it by deleting all resolutions below 4096x2160? Where do those get stored? I want to just delete them all so it can never go into VGA mode anymore.

In exploring that tool's forum, I ran across this:
 
http://answers.microsoft.com/en-us/windows/forum/windows_7-hardware/windows-7-movesresizes-windows-on-monitor-power/1653aafb-848b-464a-8c69-1a68fbd106aa
 
So I went into the registry and found numerous duplicate entries that contain monitor resolutions that are 640x480. I pared down the number of keys to just two (out of a dozen duplicates with wrong resolutions).
 
I rebooted. And.. for the first time, it booted with the proper screen setups!
My guess: every time I installed a graphics driver, Windows added another key with duplicate setups. But for some reason, many of the setups have 640x480 in them. When Windows boots, it probably chooses one of those keys at random. Since most of the keys were for the wrong resolution, it came up wrong most of the time.

 
Cleaning the registry every so often makes a difference.

Time to use the CRU tool. 

I tried the CRU tool tonight and it screwed up my system to the point where I had to spend hours doing an image restore from the last backup image. The result of CRU was no raster on the 4K monitor. Sure, my main 2,5K monitor came up like it should, but the 4K was dead. The backlight was on, but the screen was black.
Another problem was that there's no support for 4K in CRU. The best I could set was UHD. I have to make a custom setting and when I do, the OK button is disabled and I can proceed no further.
 
The system was okay for a few days, but Supermicro tech support had me make a change to the CPU EIST settings in BIOS, in an attempt to improve the frame dropping stuttering problems, and after I did that, the monitor problems came back permanently. Every time I straighten the mess out (7 minutes to fix), the next reboot its back to an invalid non native scan rate on the 4K monitor and my entire desktop has been shifted to that monitor. What's worse is my Wacom tablet settings get messed up and I cannot do anything because I can't control the mouse pointer when this happens.
 
The fix that worked for several days was to delete registry keys for the 640x480 resolutions under Graphics Drivers... Additional Mode Lists. But now that's not working. Every time I boot, a new key gets added with VGA resolution in place of 4K for the big monitor. I even tried setting permission for that hive to Deny to the system, but it changes them anyway.
 
What's scary is that after a full C: drive image restore, the problem remains. So something's wrong with the hardware, not the Windows config.
 
So far, this system has been a $6500 white elephant--a month of tech support, troubleshooting, slow performance, monitors getting switched around constantly, and not one iota of production work done. The ultimate time sink. And it's too late to RMA the stuff. I just tried to file an RMA with Newegg and the site told me it's past 30 days. So I am stuck dumping the system on eBay and getting what I can for it. Or partiing it out and selling individual components.
Very. Frustrated.

I've got to set up RMAs with numerous manufacturers:
 
Supermicro (motherboard)
EVGA (Titan X)
Samsung (memory DIMMs)
Noctua (cooling devices)
 
I can probably keep the case and use some other motherboard, maybe put in an overclocked i7-5960X and get it to 5.5GHz with cryogenic cooling or something like that. The whole system is just fraught with problems. And I've just made the first payment on the loan for it this week.
Even the minor stuff, like the fact that it takes 2 minutes to POST and when it finishes, the displays shut off and I can't see Windows boot menu, nor when to press F8, now this monitor scrambling problem, on top of the fact that it's not really any better at editing video than my 7 year old workstation with a Core2Quad. In fact the Core2Quad doesn't drop any frames when editing 1080P footage. This new system drops frames here and there for no apparent reason. I even experienced frame dropping with DV footage last week. That's just not right. And nBench results for my old CPU and the new Xeons were disappointing. My Core2Quad beat the Xeon on floating point performance in nBench. I did not expect that. Same with the memory benchmarks.. 1132 for the C2Q.. 960 for the Xeon system. Leaves me feeling that Moore's Law is just a fantasy.