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I tried a work around of adding the "Force polling using workspace" as an "Additional behaviour" in my git SCM definition of the windows job.
If the poll runs on the Linux node (the master) but somehow decides it needs to use the Windows git configuration to poll the master, that might cause the Linux master to attempt to execute git from the Windows git location, instead of the Linux git location(which is what is happening in my project). That would be a bug, and I was surprised at this bug, since there are many installations of Jenkins git which use a wide mix of Linux and Windows slaves.
I'm was not aware of such a bug, but since the "Force polling using workspace" resolved the problem for you, it may hint that is an area for more investigation.