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To have the job queue multiple builds, you might try the "allow concurrent builds" check box, in hopes that would not optimize away the second request to build.
I can't test the github push mechanism because I'm not willing to expose my test Jenkins server on the public internet, and I'm not willing to configure and expose a reverse proxy on the public internet.
I can only guess that the key difference is between the GitHub push notifications that you're using and the simple git hook based notifications I'm using. I removed the GitHub components from the bug report because I assumed it was generic to the git client plugin. You'll probably need to put them back, or confirm that you can see the problem without requiring a GitHub push notification.