Jenkins jobs going missing
Here's how you can get more info: http://[jenkins_server]/log/ -> Add new log recorder -> enter a name of your choice -> OK -> Add -> enter hudson.model.Run as Logger -> set Log Level to all -> Save.
Now http://[jenkins_server]/log/[your log name]/ will provide you with more info as far as running your jobs is concerned.
As long as the bugs https://issues.jenkins-ci.org/browse/JENKINS-15156 and its linked ones are open, it will happen in certain cases. It does not matter what you use for parallel building or dependant building... it is just core problem. Leave it or Live it.
I doubt additional logging is a fix or answer to your problem.
My answer would be - debug and send patches to devs.