Possible motherboard failure (Internal clock issue)

Hey, been having issues for about 3 months now where all applications seem to run in slow motion (High fps, just everything moving at about 80% speed usually). It doesn't happen all the time but when it does the motherboard bios is usually pretty laggy. I've tried replacing the CMOS battery 3 times and all 3 time's it's fixed the issue until I reboot the PC. I can't find anyone with a similar problem to mine as everyone else seems to be able to fix it by just replacing the CMOS battery. Can anyone help me with this issue please?

Currently tried;
Formatting my main HDD
Reinstalling GPU drivers
Not overclocking my CPU
Cleaning my PC for dust
Scanning for malware
Replacing the CPU thermal compound
Lying the PC sideways (Heavy GPU might have damaged the PCIE slot)
Replacing the PSU

My CPU and GPU temps and utilization seems fine, about 50% utilization in most programs and about 45 degrees for the CPU and 60degrees for the GPU.
I tried using Performance Test 9.0 and a few of the tests failed due to a timeout issue and the rest of them I scored ridiculously high both of which are signs of internal clock issues apparently, according to an admin on their forums, but whenever I've seen people with internal clock issues they usually report a loss of time but my PC seems to keep the time perfectly.

Any info would be greatly appreciated, thanks.
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