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I've updated Jenkins as well as Jenkins GIT plugin and GIT itself, but nothing helped. I also increased the GIT plugin timeout to one hour (using -Dorg.jenkinsci.plugins.gitclient.Git.timeOut=60 parameter) but no change either. Simply, the jobs sometimes run, but most often, they fail with the above mentioned error.
What I found really weird, and what's probably connected to this issue, is the number of git.exe/ssh.exe processes, which stay open (see the attached screenshot). All of these processes point to the (failed) Jenkins jobs. If I kill all these "hanged" processes, and then manually run the jobs, they all work!
I found this discussion, where is mentioned a "workaround" to kill the SCM processes...
http://stackoverflow.com/questions/10732940/git-operations-occasionally-hang-in-jenkins-on-windows
The problem is that it kills all processes, so it's useless in my case, because I don't want to kill processes from working builds.
Any other idea?