Does anyone know a better way to deal with this? I was thinking there might be a way to use wait/notifyAll, either in the Fork and Join activities, or with the Join activity notifying the main thread in the driver class.
Yes. We have to "foreport" the join solution from jBPM 3.2.9 (see JBPM-2790) to jBPM 4.4. For the time being, try setting the continue attribute to async or exclusive in the join activity in order to reduce the window of opportunity for a locking conflict.