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As an update to this, we have a bug in a script of ours which redeployed our build slaves. But even after this (also with both TCP and SSH keep alives enabled) we're occasionally seeing this bug. One possible explanation is that it may be related to the load on the Jenkins master. That's something that's been mentioned earlier in this case as a possible cause and something that we noticed too - Updating from 1.489 to 1.509.2 caused significantly increased load on our jenkins master. So we've given the master some more resources and tweaked jvm opts a bit to see if that improves things at all.
@Zhijun: out of curiosity, how is the load on your jenkins master? Is it at all swapping?