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I see this same bug, using a Jenkins 1.565 machine with 14 git jobs, about 2/3 of which use randomized ten-minute polling ("H/10 * * * *"). The machine sits behind an inflexible corporate firewall, and the git repo is hosted outside the firewall, so there is no opportunity to use per-commit notifications, much as I'd like to.
I started noticing missed builds late last week, when we were using Jenkins 1.559. Now that I know what I'm looking for, I start seeing stuck jobs reported by hudson.triggers.SCMTrigger within an hour or two of restarting the daemon. We've been adding 1-2 jobs a week for a couple of months, and seem to have hit some kind of tipping point.
The Groovy scripts that people have posted in the past appear to be ineffective. This one: