Now someday this may save some of you a lot of time and hassle, unless this is somewhat common knowledge but it threw the techs at Stern for a loop.
On my X-men I got the message about a software mismatch and to contact Stern. Thinking I screwed up on the code update I did it again and got the same message. Called Stern and they had me send back the main board. They got it and called and said it worked fine for them and they sent a new one back anyway. Put that in, same message. They didn't know what it was and called me back later to suggest I swap out the driver board with another Stern. Well first we looked at this board closely and noticed two fuses were blown, the audio 12 &13. So replaced these and they blew up again upon startup. So figured it was a pinched wire and sure enough, the wire for the topper was pinched by the backbox. Put in two more fuses and game fired up and the mismatch error disappeared! So all this hassle over fuses, and why doesn't the pinball say this was the problem instead up putting up the software mismatch error? So if you blow a fuse this error message could come up, and it's most likely not your main board.

This didn't happen after putting the laseriffic topper in, but later I moved the pinball and put the backbox down for clearance. I probably turned it back on a few weeks later and noticed the message and by then didn't think it was the topper as the message on the screen has nothing to do with the problem. In my humble experience when a fuse goes out, things just plum don't work but getting this message, a blown fuse never crossed my mind.