What are the bonus lights (just above the flippers) doing when this happens? Do they correctly count down to zero and keep awarding bonus? Do they get stuck at a particular value, and later continue?

I seem to remember another post or two about a similar situation and the Hole sw. was involved. You may want to search here for it. Have you noticed any movement from in that area as bonus is running down?

Capture (resized).png

If the bonus lights count down correctly and the 1000s are added correctly and then the bonus lights stay on 0 while a few more 1000s are added, check the adjustment of the Zero Position switches on the Bonus unit to make sure they're clearly opening when they should.

For a switch to work 3 things are necessary:
1) When open, there should be a small space between the contact points (duh)
2) When closing, the long blade's contact point should push the short blade's contact point enough to move the short blade
3) The contact points should be clean, which they usually will be if #2 is happening