You are seeing jobs in Tower which were launched by Jenkins stuck in a pending state? Can you add more details to this? i.e. what version of Tower are you on. What version of the plugin are you using? Also, can you manually invoke a job in Tower and get it past the pending state?
The pending state in Tower means that the job was requested but its waiting to be scheduled (actually run) within the Tower cluster. Once the jobs is scheduled in Jenkins, nothing else is done on the Jenkins side other than monitor the job.
Jobs getting stuck in a pending state would indicate (to me) that there is some kind of issue with your Tower installation.