For starters, I am impressed you can have a long mulitball on Nineball!!
Mine will do the same occasionally, and from what I can make out it is the balls not rolling down the outlane trough and getting 'stuck' on the top switch. If ANY of the trough switches (on-field chute on the left and outlane trough) are not behaving the game can get confused. The Altech will have the latest ROM code, which seems to work well as long as the switches are working correctly and it can keep track of where the balls are. I remember 'back in the day' with earlier code revisions the game had a mind of its own, and if you were lucky it would just keep spitting balls out
Try taking the apron cover off and putting balls in at different speeds and angles and seeing if they get hung up on the switches.
cheers
Ian