Pinwiki claims that surface mount nvram (of which the pinitech version definitely is... pretty obviously!) doesn't have issues with diode D1 causing too much voltage drop for the nvram to 'unlock'. You can put the NVram back in and jumper around diode D1 temporarily and see if it fixes the nvram issue.

I'm with everyone else who said the socket may have gotten damaged with the machine pins, I really don't care for the round machine pins on the nvram, unless they're going into a machine pin socket. (I prefer dual-wipe style sockets as original).

Any behavior observed (random flashers, etc.) is not going to tell you anything specific other than that the ram isn't working correctly. It's going to be random behavior. Ram has to have all its address and data lines correct or it's just not going to work correctly. The ram in system 11 not only stores the audits and adjustments but it's also the main system ram.