At this point since you appear stumped, I would try to get a SPARE DRIVE (at least 60GB) and put a clean Windows install on it. Just to test.
I'll assume W10 for the explanation.
First, try an In-Place Upgrade:
1) insert 8GB or larger USB stick
2) download and run MS media creation tool
https://www.microsoft.com/en-ca/software-download/windows10
3) After finished, run "setup.exe" from the stick
4) choose to keep "data and applications" if asked though it should be greyed out
5) do not enter a key if prompted, just skip
6) finish, and let it redo any Microsoft Updates (check at Settings-> Update & Security.. )
does not fix the issue?
7) shut down PC, unhook all drives except add a new blank SSD or HDD of at least 60GB (want at least 120GB if using long-term)
8) boot with USB stick still inserted to run W10 Install
9) SKIP key when prompted
10) Don't LOGIN as it's just a test (I think Microsoft did so for me though... added my user name and password. sigh)
11) TEST
*If it works then your issue was a SOFTWARE problem with Windows. Sometimes they are hard to fix. I spent many HOURS trying to fix it on Windows 8.1 then the W10 upgrade fixed it (bad audio). Then it came back with W10 and I fixed it with an In-Place Upgrade but I couldn't fix it any other way (and I've tried that on OTHER computers with the same issue and the In-Place Upgrade did not work).
If the PROBLEM still exists it's a hardware issue, though I doubt it's hardware.
So if the CLEAN INSTALL works you may want to consider planning carefully for a CLEAN INSTALL. If you do that I'd then make a BACKUP IMAGE, preferably do an automated solution, weekly using Acronis True Image. (i.e. Incremental, with auto-deletion of older backups, 2nd highest compression... )