We're using the branch API build throttle, limiting builds to 12/day. A newly triggered build happily sits in the queue. The only way for me to force the build to happen now, rather than in (at most) 2 hours, is to change the job configuration. Clicking on "Build Now" on the job in the build queue changes nothing.
Clicking "Build Now" on the job waiting in the build queue should trigger the build immediately, regardless of build job throttle settings.