Steps to reproduce:
1. Create a parameterized alpha job with Git support. As in attached screenshot.
2. Enable "Execute concurrent builds if necessary"
3. Launch first alpha job with specific commit.
4. Wait for it to start running some jobs, but still have some left in queue.
5. Launch another alpha job with a different commit.
6. Those jobs, which were running will be requeued to run again with for the new commit. This is as expected. However, those jobs, which were still in queue, will not be queued additionally, because Jenkins somehow thinks that they are exactly the same.
7. The end result is that some of the jobs will be run for one commit, while some for 2 commits. Instead of having 2x runs for the same amount of jobs, only 1-2x runs will be made, because some of the jobs won't be rescheduled to run with the new parameters (commit).

http://stackoverflow.com/questions/11089133/is-there-a-way-to-avoid-duplicate-parameterized-jenkins-builds also describes the same issue.