Firstly, have you double (and triple) checked ALL ribbon cables to ensure they are all on correctly, not reversed, and not offset at all?
Don't laugh, but try this as well :
Remove your CPU. Place it flat on a table atop a piece of corrugated cardboard (like a collapsed box).
Put both thumbs on the square WPC ASIC chip in its socket and PRESS FIRMLY.
You should hear a nice solid kee-runch as it seats in the socket.
Reinstall CPU, see if there's a behavioral difference.