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Yes I have noticed the problem several time, it led me to disable JaCoCo completely in mid December.
I triggered the second build myself because I was surprised if failed the first time (it was ok on my machine) so I triggered it again to see if it continued to fail, I was surprised that it did with different coverage report.
The logs are coming from the build execution on jenkins, and yes I was using JaCoCo maven plugin to set the thresholds.
Again, I did open an issue on the jenkins plugin because I never had any inconsistent coverage report when building locally (at least I never identified one) but I'm not sure at all the problem comes from jenkins plugin.
Note that I don't work anymore in the company where I had the problem, it will be thus difficult for me to reproduce it.
One last thing, I'm using JaCoCo for an open source project of mine (AssertJ) and did not encounter such problems, the difference between AssertJ and my last project was that AssertJ is not a multi module maven project.
And by the way, I wish you and all others jenkins guys an Happy New Year.
Joel