Question PC taking several minutes to boot after GPU issue?

Jan 23, 2021
Hi all, my specs are:
MSI B550-A PRO ATX AM4 Motherboard
AMD Ryzen 5 5600X 3.7 GHz 6-Core Processor
ID-COOLING SE-224-XT 76.16 CFM CPU Cooler
Crucial Ballistix 16 GB (2 x 8 GB) DDR4-3600 CL16 Memory
ADATA XPG SX8200 Pro 1 TB M.2-2280 NVME Solid State Drive
Samsung 850 EVO-Series 250 GB 2.5" Solid State Drive (I boot from this, Windows 10)
MSI GeForce GTX 970 4 GB GAMING Video Card
Fractal Design Define 7 ATX Mid Tower Case
EVGA G3 650 W 80+ Gold Certified Fully Modular ATX Power Supply
LG 27GL83A-B 27.0" 2560x1440 144 Hz Monitor

I've upgraded my whole system recently, with the most recent change being my CPU cooler (a week ago). It has run well since then, but yesterday, when I started my computer, the white VGA light on my mobo was on solidly, and there was no display, although all fans (including the GPU fan, and light, worked). Occasionally it would freeze when restarting, and sometimes I got the error message that I need to connect my PCIE cables to my GPU. Sometimes,
after about 10 mins of leaving it, it boots. Today, the same thing happened, so I tried various things (listed at the end), and now the white VGA light doesn't seem to appear.

But now, when I turn the computer on, I get stuck at the BIOS page for several minutes, before the loading circle appears for a while, and then the computer finally boots, so clearly there is still something wrong. Temps are all fine after booting, and I can work / play games on it as normal with no issues. I have assumed because the original issue seemed to be GPU related, it may still be the issue, but I'm not sure. Note, when building this initially I already updated my BIOS to a version that the mobo supports the 5600x. It has been working with it for several weeks.

The steps I tried while trying to fix the original white VGA light issue:
  • reseating the GPU
  • re-connecting PCIE cables + other cables from PSU and mobo
  • re-connecting the aftermarket CPU cooler (I did notice temps have dropped from ~40 idle to ~35 idle, probably better thermal paste application)
  • changing displayport 1.4 to 1.2 on my monitor
  • disabling PBO (from auto to disabled)
  • update GTX 970 firmware to support displayport
  • make sure drivers are up to date for GTX 970
I need this PC for work every day, so I'm hoping it doesn't get any worse, and obviously I'd like to work out what the issue is. For now it awakes fine from sleep mode so I'll try avoid turning it off. Any help will be massively appreciated, thanks!