Ok, this is going to be a WOZ specific suggestion, because I went through this for months...
Setup a video camera and play the game. If this happens after the left VUK fires, it is the Crystal Ball causing the I/O board to reset.
This is specifically if it isn't starting the "end of ball" stuff. In my case, the Crystal Ball was installed with the wireform ramp leaning on the connector. Over time playing the game, the pins on the CB screen broke, however the connector was hot glued together, so it seemed very tight. When the VUK would kick, that shake caused the inside pins to disconnect sometimes, and that would reset the I/O board which took a couple seconds to boot.
Even if it was only with another vibration it could be the same thing. For mine the ball was always coming down the left wireform to the left flipper when it happened. Once I cut off the glue and pulled the connector, I found my issue.