I believe this happens due to floating point number inaccuracies when converting the item from the multiprocessor into flow units on the mass flow conveyor and back. The first time an item leaves the multiprocessor no item is actually generated at the end of the mass flow conveyor. Then at a later point, two items are generated from one "batch". You can also see is the "double step" in the output vs time chart of the combiner at around 12:15.
Other than removing the mass flow conveyor (is there even a point to it other than visualiziation?), the only workaround I can offer is to change the "Units per Package" setting on the exit transfer to something like 199.99999. This will result in an extra item being generated after a very long run time though.
