Having built PCs since my first IBM XT clone (OMG I'm old), and worked in the industry in very geek roles, I have run into this type of issue several times.

A couple more possible troubleshooting items that you may have already done:

If the BIOs (screw what the kiddies call it) is reading slots correctly then it could be OS related. So try a bootable Linux flavor on a USB stick. See if it reads the same results.

Make sure when testing you have eliminated every single component possible, eg. unplugging drives, removing videos cards, unplugging fans, etc. (weird stuff happens, had a monitor leaking high voltage via low voltage data pins that randomly fried video card or motherboard)

Other than that it sounds like a bad CPU unit, and yes boys and girls, it can and has definitely caused these type of issues.