Also, if you're going to do any speed scaling adjustments, go ahead and start with the MSU zeroing procedure. It's simple and can make a big difference.
Most of the really intermittent issues I've had like this have come down to ribbon cable connections, Molex & card plugs too but especially the ribbon cables. Except the last one was an MSU board. If you let the car cycle and gently tap plugs, move wires, flex cables, etc. sometimes you get lucky and catch it. I like to clean ALL the plug connections on Miprom 21s with De-ox-it and look in the ends of the Molex connectors for distorted/tweaked terminals. I replace the bad ones with the gold plated "Trifurcon" terminals that grab the sides of the pin too (same ones I use on Ascension Power supplies & Accu-Flite SCR plugs.