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While writing tests for the git-client-plugin, I found a bug in the command line git implementation used for remote polling. The bug is fixed in git-client-plugin 1.6.2 which was just released.
It is worth trying git-client-plugin 1.6.2 to see if it resolves the problem. Refer to https://github.com/jenkinsci/git-client-plugin/commit/e5e75d5a100905c0d5b332bbde3642e96ffe10a9 for more details on the remote polling bug.