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I went back to old versions of both Jenkins and the Git Plugin, to no avail.
I identified that wish.exe was being executed by gitk.cmd, but not terminated, I had hundreds of open processes over the course of testing.
In the end, I added a tool location of Git(default) to use git.exe (instead of gitk.cmd). This resolved the issue. I did this with the latest version of Jenkins, but git plugin versison 1.1.14. I intend to try using the latest git plugin with this override next.
Its unclear to me what was wrong with executing using the gitk.cmd as this cmd used to be required to ensure the processing environment of Git was setup correctly on windows.