The issue depicted in blocked_threads.png appeared in our production server.
(it results on a broken state that we fixed by rebooting the server)

The result of the first investigation is the following:
cleanUpGlobalClassSet
https://github.com/jenkinsci/workflow-cps-plugin/blob/master/src/main/java/org/jenkinsci/plugins/workflow/cps/CpsFlowExecution.java#L1037

seems to have compatibility issues with the memory leak fix implemented in groovy 2.4.8
https://github.com/apache/groovy/pull/219/commits/f7c688e101af77170448cf0be9103c4e6dac3f74

It seems that gradle had a similar issue, that was fixed by the following commit in groovy 2.4.8
https://github.com/apache/groovy/commit/82c9d20a160c7e4f59630f163a68df82f5e0eba4