A bad 5101 can certainly cause what you're seeing. It's probably the most commonly and easily damaged chip in all of pinball.
An NVRAM replacement will not be so sensitive, last a lifetime, and require no batteries ever...
www.LockWhenLit.com/anyPin.htm
Check continuity from diagnostic switches to CPU. With your description though, definitely sounds like a bad 5101.
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Rob Anthony
Pinball Classics
http://LockWhenLit.com
Quality Board Work - In Home Service
Borygard at gmail dot com