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When writting into the System.err stream (and probably also to System.out), the content of output window can be incomplete. After doing System.err.flush(), it's OK. Sure happens for System.err and external execution.
release 3.1 [20]
fixed in main trunk - caused by a race condition
It looks OK in release 3.2, build 38
Resolved for 3.4.x or earlier, no new info since then -> closing.