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That might be possible – we're seeing something odd with multi-branch builds, too – it seems like GIT_BRANCH always lags behind one build on what its value is.
That is, starting out, if we push to branch A, Jenkins builds branch A, then if we push to branch B, Jenkins builds A, then if we push to B, it'll build B. Hmm, how to write this? If our push sequence is A B B B A B, Jenkins will build A A B B B A – essentially it's seeing the prior build's value of GIT_BRANCH. Something like this.
We evaluated switching away from Jenkins to Atlassian's Bamboo because of this issue, but they don't have the ability to integrate with Github triggers for building branches correctly (just polling), so back to Jenkins and manually fixing this (which is annoying – writing a job that accepts the trigger and then makes API calls to Jenkins to add the branches as new jobs).
-Jeff