I saw you posted this in the seam forum as well. The discussion should be done at least at one place (crossposting is not handy) and since it is (imo) more closely related to how seam is using jbpm than a jbpm core issue. I might be wrong but we should at least discuss it in one place.
(I think btw it could be related to not saving the processinstance (e.g. because a transaction is not ended) but that is just guessing... A debug trace would be handy, but analyse it first please and do not post it completely)
Right on kukeltje; sorry about the crosspost.
Instead of using the Seam ManagedJbpmContext and outjection to the business process scope, I used the good-old JBPM API to launch my process and set context variables manually. Since then, I have not been able to reproduce.