I'm not sure how it happens, but suspect logic issues in the wiring or items disappearing from belts, which can cause the same effect.
The symptom is, the final output is less than full belts, so when I go back to look for the problem, I see (image 1), bad parts coming off the line (and getting trashed) from the upstream stackers. But after staying in the area for a minute, it works perfectly again (Image 2). I have gone away and come back several times, so the problem is constantly repeated itself.
The timing of this it is, if shapes going into a stacker detect nothing coming from the other side, they will continue on as a single, and not wait at the stacker.