With our Blitz, the buttons at the door are cut...trashed, so we have to in through the back to adjust the settings on the board itself with the dips.
I was told you don't have to shut the game off to do it, and it does work, and you can adjust it all from there. That way, if the battery was bad, the settings would be fine and stay where you put them, unless you shut it down.
The issue you are talking about seems to be beyond that. Never heard of one doing that before. Maybe the new flash drive is causing it to goof off?