The fact that it was allowing the flippers on (at full strength) during attract mode and randomly firing coils makes me think that something is wrong with the MPU.  It sounds like screwy control messages coming through - but I guess you are right, voltage weirdness can do weird things too.

Read this Matt: http://aussiepinball.com/index.php?topic=6645.msg88968#msg88968
Strangely enough the flippers were active on the Trident after it reset until the board fully restarted.
Might be totally different, but it would be weird if you did similar to what i did when you changed the EOS?????