Regarding the 2pin vs 3pin.
I only mentioned it because another user solved their problems moving to 3pins on all plugs. They were even seeing small sparks when connecting usb cables!
So, maybe don’t discount it immediately.
Just for clarity, the cause you are suggesting is also just as likely to be right.
It might also be related to these problems:
And also possibly the DP failing to properly negotiate swing and pre-emphasis.