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I wasn't clear enough with my question. Are you using the default git provider ("Default" - which uses command line git as its back end implementation), or the "JGit" provider ("jgit" - which uses the Eclipse jgit implementation as its "back end provider")?
You can tell which you're using in the job definition. If there is a pick list to choose your git, then read the value of that pick list. If there is no pick list, then you're using the default and have not configured jgit at all.
Also, can you use Windows task manager to search for any processes named "git.exe". If a git process blocks waiting for authentication, it may hold files open so that they cannot be deleted (on Windows).