@Patrick Zweekhorst found an interesting bug, which is demonstrated in the attached model.
The model started with a single operator attached to a resource in a global flow. In addition, the operator is attached to its own instance of a Task Executer flow. If the Count of the global flow's Resource is set to 1, everything works fine: there is a single operator in the model and the Task Executer flow's Source generates a single token for the operator.
However, if you change the Resource Count to 3, the Task Executer flow now has way too many tokens. To be precise: there is one token for the original operator, and 3 tokens for each of the copies.
Looking at the way the experimenter changes the number of resources, we suspect that
applicationcommand("recreateObjectConnections", newObj, firstObj);
generates some additional events for the Task Executer Process Flow at the start of the event list, in addition to the event that the Process Flow generates itself.