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I am reasonably confident that it is a bug in the git program (or a bug in the Windows file system and its locking design), not a bug in the git plugin.
The command which is failing with a timeout is a call to the "git" program as a separate process. The git plugin calls the git program and waits for the git program to either complete or for the timeout to expire. In this case, the timeout expired, probably because of Windows file system locking semantics.
When you say that you did not see the issue before, were you polling and/or building from multiple concurrent jobs on Windows machines previously?
What version of the git program are you running on your Windows slaves?