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A clue could be that since we upgraded the build pipeline plugin to 11088e6301 we ONLY see this happening on the first job in the pipeline and never on downstream jobs like we saw before. We have seen it hang on both SCM trigger and rebuild. Unsure if it ever happened on a plain manual trigger, but I don't think it has. We believe that it was the fix for JENKINS-21527 in 8ee14444e7 (merged to mainline in 376b460e12) that fixed it.
I think this is interesting because it highlights what was wrong and maybe a similar fix needs to be applied somewhere else.