If a branch to build is specified like REPONAME/BRANCHNAME then the git plugin will look for branches named REPONAME/REPONAME/BRANCHNAME.
Worse still, if the git repository has multiple repositories configured, it will then search for OTHERREPO/REPONAME/REPONAME/BRANCHNAME.

I believe this is the same cause as https://issues.jenkins-ci.org/browse/JENKINS-14394

I believe the problem code to be https://github.com/jenkinsci/git-plugin/blob/master/src/main/java/hudson/plugins/git/util/DefaultBuildChooser.java#L73, the block after 'if (!singleBranch.contains("/"))' should be inside it, since that is for unqialified branches.

I worked around this issue by changing the refspecs to include an extra component in the branch, so origin/master becomes origin/UGLYHACK/master with '+refs/heads/*:refs/remotes/origin/UGLYHACK/*', so the branch specification becomes origin/*/master.