1 EM's light up when you turn them on (or hit the left flipper button). They reset when you hit the credit button or add a coin. So that's alright.

2. Since you said AFTER each ball, it sounds like your "points" are coming from the bonus unit. The bonus shouldn't count down until a ball enters the outhole.

Make sure your outhole switch isn't stuck on. Check the Bonus unit zero position switches and switches on your ball index relay. And make sure you don't have any stuck on playfield switches, especially any that add bonus points.