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The answer is moving the temp dir for Jetty outside of the normal temp directory which gets periodically cleaned. If you examine Greg's pull request you can see which files to change to move the temp dir for jetty and I can confirm this fixes the problem.
To implement that solution is to edit /Library/Application Support/Jenkins/jenkins-runner.sh (you'll need su priveleges to do so) and add this line to the middle of the file near the lines that are similar:
tmpdir=`$defaults tmpdir` && javaArgs="$javaArgs -Djava.io.tmpdir=${tmpdir}"
You'll need to create a temp directory for Jenkins (/Users/Shared/Jenkins/temp in my example) and give ownership to Jenkins:
sudo mkdir -p /Users/Shared/Jenkins/temp
sudo chown jenkins:jenkins /Users/Shared/Jenkins/temp
Then you need to set that directory as default:
defaults write /Library/Preferences/org.jenkins-ci tmpdir /Users/Shared/Jenkins/temp
Restart Jenkins and the problem will be gone for good.