Is the second copy of the job triggered by polling or by a hook script which runs on each commit to the git repository?
If the second run of the job is triggered by polling, then I don't know any way to prevent the duplication (though I generally don't see that type of duplication myself).
If the second run of the job is triggered by a hook script, then you may be able to prevent that second job running by not including the "sha1=xxx" argument in the hook script. I've found that if a "sha1=xxx" argument is included in the hook arguments, then the git plugin schedules a build of that SHA1, whether or not it has already been built. If the "sha1=xxx" argument is not included in the hook arguments, then the git plugin polls the remote repositories to see if there are any changes and only schedules a build if there are changes which have not been built.
Mark Waite