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You might try a work around of adding the "Force polling using workspace" as an "Additional behaviour" in your 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. That would be a bug, and I'd be surprised at that bug, since there are many installations of Jenkins git which use a wide mix of Linux and Windows slaves.
I'm not aware of such a bug, but if the "Force polling using workspace" resolves the problem for you, it may hint that is an area for more investigation.