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We found to root to the problem. We have a windows service that launches the slave and for some reason we had enabled piping of stdout and stderr and the output from the slave.jar caused the pipes to deadlock. By disable the stderr and stdout piping the deadlock issue was resolved.
We found the issue by running slave.jar in a command line window and noticed that the findbugs plugin writes a lot of data to stdout and this was to much for our service to handle.
So I take it that at java.io.FileOutputStream.writeBytes(Native Method) is actually writing to a local stream that is deadlocked.