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With my current plugin updates (msg me for list), the problem has gone away, except in this use case:
1. Quiet Jenkins (announce "shut down")
2. Wait for all running builds to complete on all nodes
3. Queue a build of the matrix job
4. Cancel shutdown
5. Job begins building on all nodes except the one running the flyweight launcher task; build for that node remains queued in the deadlock condition.
So far it works to exchange steps 3 & 4, and hope nothing else gets queued to run between them.