One of my fellow workers claimed thinBackup was taking Jenkins down, sure enough I found that the case myself this morning.

Shutdown could not be cancelled (it would go down, but immediately be reasserted). ThinBackup had some messages about waiting for quiet mode, but there also seemed to be an exception related to cancelling shutdown, scanning with my non-Java eye, it wasn't clear it the exception was thinBackup related or not.

End of Jenkins log provided