OK, found another bug that I felt needs mentioning. While playing a two player game, I was player two and on ball 3. I had decided to just go after WHAT! mode (we were only playing for modes, not points). Played it several times in a row (not completing the first times). I think I completed it on the final pass but not sure.
Anyhow, saw a graphic that made me think the game was rebooting, however I stayed in my game and the player 1 score appeared to be zero'd out. We grabbed a quick pic of it. I was able to finish my third ball and then the final scores were displayed and player 1 actually had a score. Not sure if this is related to playing WHAT! over and over, complete coincidence or...
As for scoring tweaks, it seems like if I want big scores, all I do is go after the Add-a-Ball mode (and 1000 corpse multiball). Personally I think the add-a-ball mode should not be able to restart once it is completed unless you complete some other objective. There seems to be very little incentive to go after the other modes if you want the biggest point scores. Perhaps the bonuses for progressing through and also completing modes need to be higher.
Often with friends we play some games for big points which means we end up almost shooting at the add-a-ball exclusively or we play to complete the most modes. It's two very different games at that point.