Spandol, I have a Meteor on route with an Alltek MPU. No problems with the displays at all. It sounds like wiring problem on the display chain. Try reseating the display connectors on all displays and see if anything happens differently.

I had a troublesome issue similar to this on a Bally Star Trek that I was restoring. I repinned connectors but the intermittent display issues persisted. I could wiggle a wire a little and sometimes the display issues would go away, but then come back. It ended up that I was working at the wrong end. The bad connector pin was at the other end where it connects to the MPU.
So, verify those header pins there, as well. Good luck!