I've got the same issue. Went away after triggering them manually in test mode, then the errors showed up again after a few more games.
Just got the deadworld mod today but haven't installed it yet. Doesn't have the plastic protector in it.
I'm leaning towards believing the idea that you get the errors if you haven't triggered a six ball multiball. I haven't actually played a super game yet. What makes it more believable is that these errors weren't there when I picked up the game earlier this week. The couple that I bought it from knew nothing about fixing pins, and had never seen the playfield raised (and didn't know there were menu options).