Ps4 controller will only work correctly in safe mode

So… I am new here, Hello.
So, I bought a ps4 that the USB ports weren’t working on. So I was going to replace the ports, then move on to the ic if that didn’t work. The ps4 was reset to factory and not yet into the system. So, when I connected the controller, after a few reboots and tries, it went past the " connect ps4 controller and press the ps button screen" by a few screens. Then it would do this kind of highlight blink around the selection when I pressed X. I have seen this before with a bad hard drive…Once. So I just put in a spare, put it in safe mode and WOW… the controller worked on the safe mode selection. Perfectly. I initialized the hard drive and used the USB to reload the system… success. It reboots and same issue. It just kind of blinks when you hit x. So I cant understand whats going on here. 3 possibles:

  1. The spare drive is bad too and find another. (I have a few, will try tomorrow again with different drive)
  2. the USB port or ic is bad and safe mode bypasses something.
  3. There is something I am missing.

So, has anyone had this happen before? If so, please tell me the fix. I fix ps4’s and xbox one very frequently and this one has me stumped. HELP!?!?!?!?

I have also reset the controller. Just fyi

Did you find a solution??? I’m having the same issue.