Hard to know what you're describing without video, but even when working correctly the bonus count does not have a consistent cadence due to the score motor pulses it uses:
Capt. Fantastic Bonus Count (resized).jpg
On a regular bonus count the 1000 points and chime are fired by the #2 cam which sends out groups of 5 pulses with a consistent gap between groups. On a double bonus the #9 cam is used instead which sends out pairs of pulses with inconsistent gaps between the pairs.
If you're not hearing these patterns I wonder if the teeth on your score motor cams are worn. Closing the gap on the relevant cam switch might compensate for that.
/Mark