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Another update regarding my previous post.
When I inspect the hung git.exe process, using procexp, I can view the "Environment".
I can see that the "HOME" directory is set to "/var/lib/jenkins" rather than the usual "C:\users\git".
So it appears that Jenkins master is passing through the HOME environment variable as it's own (which it is in deed /var/lib/jenkins on my linux master)
which is blowing away the usual HOME environment variable on my windows slave.