I've started a topic on tomshardware, but might as well try here too:
http://www.tomshardware.com/answers/id-3609023/constant-video-stutter-display-problems-caused-gpu.html

In short, the problems happen:
Randomly, decided at boot time (don't get better or wrose till you reboot)
If they happen, they do so before Windows loads (even at BIOS)
Only on PCIE GPU (not on mobo's integrated one)
With 2 different GPUs I tried - one was brand new

Tried:
• Moving the graphics card to different PCI slots. Many times.
• Playing around with different video card settings. Some settings would alleviate the problem on some software, but nothing would solve the core issue.
• Changing NVidia drivers. Updating to the latest, reverting to older ones. Installing them completely from scratch. The problem happens even if there are no nvidia drivers installed.
• Playing around with all the different BIOS settings I could find. All the obvious and less obvious ones.
• Different monitors. Different monitor cables.
• Switching between DVI and HDMI.
• Memtest.
• Checking cooling, fans... etc Temperatures are normal when problem happens. Both CPU and GPU. Even when stress-testing both.
• Different PSU cables.
• Updating BIOS.
• Updating HD firmware, checking HD using Samsung Magician.

Any idea on how to proceed? I'm thinking of 3 options:

_ Replacing PSU:
Pros: easy to do. Little work involved - just replace the PSU.
Cons: low chance of success - it's my experience that bad PSU causes shutdowns or failures to stop altogether; and don't affect performance. If it's not the case, I'll be stuck with an extra PSU that I unnecessarily bought.

_ Reinstalling Windows:
Pros: no money involved; no extra parts to buy.
Cons: More work involved; backing up everything, reinstalling software (plus Microsoft stopped supplying Windows 7 iso's unless you have a retail key; I have an OEM one and don't have a recovery CD). Also low chance of success - I think if it was a Windows problem, it wouldn't appear at BIOS before Windows starts.

_ Replacing motherboard:
Pros: I think this has the biggest chance of success.
Cons: Most work to do. Reassembling the PC, and putting it back together, and boy installing the heatsink+fan on my CPU was a pain by itself. On top of that, a Windows reinstall might be needed too. Plus if it's not the case, I'll be stuck with an extra mobo that I unnecessarily bought.

Thoughts?

Does it sound like a motherboard problem? Could all PCIE slots be damaged? Could it be the PSU after all? Anything else altogether that I could try?

What are your suggestions?

Have you tried unplugging power cable and internet and leave it alone overnight?

I have seen a similar problem in the past. The first thing that comes to mind is you could be having latency issues caused by a bad driver or (since you say it affects the BIOS) hardware conflict, such as a shared port, memory address, IRQ and/or DMA. I used this DPC Latency Checker to diagnose and fix that particular problem, but it was a long time ago and I don't remember specifically what was conflicting. Maybe it will lead you to a solution?

Have you tested your video cards on another computer? Have you always had this problem or is it something that just started happening? It could be that your motherboard has a problem. I've had blown caps cause similar issues.

First thing that jumps out at me is a PSU issue. It sounds like the card isn't getting enough juice.

If you have a modular or semi modular PSU, try switching its rail to the other one. I have my motherboard, cpu, and gpu on one rail and everything else on the other (At least I think that's how I have it set up.... I'm too lazy to crack open the case right now)

Good luck!
-Cym

Thanks, but I don't think that's the issue. This kind of conflict would not cause the problems occuring the way they do: randomly at booting, constant after booting. Also "The problem first started appearing a year and a half ago, but it was so small I ignored it. Initially every 8 or so reboots I'd get a tiny stutter when playing videos, so I'd just restart the PC to make it go away. It gradually got worse, till I'm now in a stage where I sometimes have to restart the PC several times to have it boot without the stutter."

That's more indicative of hardware failing over time, than a driver/hardware conflict. Thanks. The PSU if fully modular, and I already did try before using different cables and moving the cables around, but the problem occurred nonetheless.

However, I just made a test and had the GPU connected to the PSU to 3 different slots and booted the PC 10 times on each slot. The problem seemed to occur significantly more often on on of the slots and less often on another.
I'm going to do more testing tomorrow to see if these differences are statistically significant or just flukes. If they are indeed variations, this could indicate the PSU is at fault and will warrant buying a new PSU to try it out.

(fingers crossed it is the PSU; that's the easiest thing to replace).

Sorry just got back to GOG. Did you test yet? I'm hoping it's the PSU. While the mobo is fairly cheap to replace depending on model, the PSU is way cheaper and easier, like you said.

Let me know!

Fingers crossed!

there seems to be a repeat of the early 2017 windows 10 game mode bug with a recent patch they put out, so it probably broke what they did to fix the crap they did last year Seriously thinking of going BACK to windows 7 and saying F it....

Seems like something I dealt with before, re installing windows does the trick most the time when it comes to odd issues like this. or the worst might be the motherboard. if re installing windows does not fix it then it's on a hardware level. PSU does not effect this at all, Try flashing the bios to an older version then flash it to a new version

so many little things to try and see but my shot at the hole is motherboard issue.

Im using Windows 10.
Its almost certainly hardware. Happens before windows loads.

Tried flashing bios many times already.

Monitors' specifications? What resolution do you use?

I suspect that your GPU is too fast for your monitor.

1920x1080. Its an iiyama, forgot the model.

Tried on a different one too from a friend. Forgot the model.

Can electric current fluctuations produce such stutter? An APC UPS is always a good investment.

An easier method for testing if it's from Windows or not, is to make an image for your Windows partition, then install a clean Windows. If the reinstall doesn't resolve the issue, you just restore the backed-up image.

What series board you are using? model of board. Hope replacement does not cost you much if it's older and gotten from ebay or something.