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I believe the failure case you're detecting is for the case when a "fast remote poll" is used with the command line git implementation. The git-client-plugin needs to create a temporary local git repository for its operations, but makes the mistake of not generating a completely unique directory name.
I assume JGit works reliably because it creates the temporary directory with a unique name each time.
The problem will likely only be visible on Windows due to the more restrictive file locking rules of the Windows file system.
The problem is not detected by any of the unit tests in the git-client-plugin because it is in an authentication area and there are currently no authentication tests for the git-client-plugin. I hope to learn enough about authentication in the git-client-plugin to create many tests for it, but it has been very slow progress.
If you want to test my theory, you should be able to cause the problem to be consistently repeatable if you create a plain file named ".git" in your system temporary directory. Something like
Once that plain file is created, I believe the attempt to call "git init" for remote polling using command line git will fail consistently.