I forgot that this job tries to check all branches as well and I wonder if 
that is more of the cause. The credentials are stored within the local 
repository so multiple Git repos probably wouldn't cause conflicts. 
However, if a single repo checks out multiple branches, it of course does a 
git checkout so the same .git folder is used. I'm created some test jobs, 
one with multiple SCMs and one with a single SCM, both configured to check 
all branches. So far I've not seen these same issues. I still need to make 
sure the same version of Git is being used between the test jobs and the 
problem job.

I would also add that although it is intermittent, once it gets in this 
weird state it stays there until we manually run the job.

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