Windows reset everything - Start menu - audio - etc?

My sons PC has just been having odd issues... this is the newest.
Booted.... it got to the lock screen (kind of) - and had the power icon in the corner. We chose restart
Seemed fine... start chrome. Froze
Force restart... start chrome. Froze.... ok chrome is messed up
Force restart... uninstall chrome - kill the settings file... re-install ok.
Start menu is missing some stuff?
Popup states drive error, restart...
restart... boots fine. chrome works... but the start menu is empty. like EMPTY of all the things he had in it.
Only shows ALL APPS, and Power, and 2 blocks (for windows store and edge)
He starts discord... audio settings are gone. He has to re-pick the devices.

Thats all we have found so far... im stumped as to what is going on?

on a side note, anyone have USB 3.0 issues with Gigabyte 990fxA-ud3?
Thanks!

If you are still having these problems I would suggest a repair install with an in-place upgrade:

https://www.tenforums.com/tutorials/16397-repair-install-windows-10-place-upgrade.html

Yeah i will pass on that unless really needed. I just did a fresh install about a month ago on his system.. he has had weird issues since we got his computer. I have been using Win10 since launch and have had very few issues... his system has been plagued.
Freezes, stutters, USB issues, etc.. The only major difference between our pc's is that his is an AMD build, mine is Intel.

OK. Driver problems of the graphics card or motherboard are usually to blame but also the manufacturers can provide a lot of bloatware some of which can also cause problems. I would remove anything that is not essential and then try troubleshooting with a clean boot process and if you can get it to start properly then gradually add back in the various services and startup items until you find the one that causes the problem.

If nothing works then you are back to the method I originally suggested, it is usually the answer and the bonus is that by following that method you do not lose any of your programs or files.

Clean install was done - its Custom built pc (I won it actually) so it has nothing extra.
He has only installed a few games on it, and a few things like Razer Synapse.
I have updated the drivers for both the GPU and USB (Tried windows USB drivers and Gigabyte's USB drivers - its 3.0 only issue.)
It starts fine... its just keeps having odd issues - strangest is the usb 3.0 ports just dont work. Plug an xbox controller in, it works for about 20 seconds then stops. Headset, works... then freezes the pc up when something stops using the headset (like closing skype)
ALl of this is on a FRESH full wipe clean install of windows 10. Motherboard Bios is updated too... The guy that built it said he has heard of a usb 3.0 issue but i cant find anything.

the windows default first (to see if it worked) - then used the one from Gigabyte's driver page for the motherboard.
GIGABYTE - Motherboard - Socket AM3+ - GA-990FXA-UD3 (rev. 4.0)
(They havent updated that driver since 3/18/15!)

but I did that.. I ran clean windows with updated drivers for a few weeks. It does the same thing... Im starting to wonder if there is something wrong with the motherboard.