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I had a similar problem with my Meteor. I had original MPU200 and the problem was a mismatch between the clock speeds of the 5101s. You are using a Altek - BUT - have you set the STERN MPU jumper on the Altek board ? If it is set to BALLY, it will give you strange problems like you are describing.

The other issue might be the ribbon cables from the Altek to the Soundboard.

I had an issue with the spinner sounds and the countdown bonus sounds skipping completely.

Try the jumper on the Altek first and report back