Make sure your bonus unit at game start resets correctly at 1000 points and that your bonus end of stroke reset switch is released!

In reset sequence it resets your bonus unit going to the zero eos position then it pulses +1000 immediately after so at ball start you should have a bonus unit resting at 1000. EOS is not activated anymore but the 1000 position switch is.

You bonus unit lights should never flicker like in your video.

Multiball will most probably not start correctly if your bonus unit is wrongly set up. It excepts your bonus unit to not be a treset and have a minimum amount (1000 or more) to pay off the bonus and then release the ball.

Ow yes! this can be a problem. I had the same thing too and the timing of the bonus unit reset sequence was not ok.
The reset and +1000 was too fast after each other and sometimes was skipped this way.

If you have the problems with the ball index relay, adjust and clean contacts to be sure.