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This also happens with QuickBuild 3.0.x. This seems to be JVM issue: when two threads are started in the same time (almost), the short thread (the thread running short task) may wait for finish of the long thread (the thread running long task) for some unknown reason. I reproduced it with a very simple program.
correction:
This bug is not reproduced on QB v3.0.13 (see screenshot "durations-v3.0.13-ok")
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I have two identical configurations: on v3.0.13 & on 3.1.0-beta1, for the same project but different repos: SVN & Git
On v3.0.13 I reviewed all the builds: durations of parallel steps are different (I can attach screenshots If you wish)
But they are the same for the v3.1.0-beta1 (if steps are successfull, If failed - durations are different)