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If you're using fast remote polling (the default), and if your "Branches to build" setting matches more than one branch in the repository, then you might consider upgrading to git-client-plugin 1.10.0 and modifying your "Branches to build" to use the "refs/heads/<branchName>" syntax rather than the "origin/master" syntax. The git-client-plugin 1.10.0 release adds a way to unambiguously specify a branch name, while still allowing the earlier syntax and its related ambiguity.
Refer to Alexander Link's summary for more details.