I believe that the behavior you are seeing is by design. The concurrent builds checkbox allows you to run multiple instances of that job at all, but the SCM poller will only launch one at a time. Basically, with the checkbox you could kick off as many builds as you wanted manually.
If you really want to be able to launch a build at 12:30 in the below case, you need two jobs.
Job A monitors SCM, and when it sees an SCM change, it launches job B.
Job B doesn't monitor SCM at all. It lets job A kick it off, grabs sources from SCM, and goes to work on it. You will need the concurrent build flag on this one.
I have something similar in my own setup. Job A doesn't have any meaningful build actions, but has a post-build action of "trigger parameterized build on other projects" (IIRC, you need the Parameterized Trigger plugin). Tell job A to launch job B in that post-build action and pass any SCM information (such as branch) as a parameter. So now, the timeline goes as:
12:00 Jenkins Project A polls Mercurial and sees a change. Starts build #A-1
12:02 Jenkins A-1 launches job against project B (build #B-1) and exits out. Job #B-1 runs for the next 80 minutes
12:15 Another change is made in mercurial.
12:30 Jenkins job A polls Mercurial (since it isn't running a build on project A) and sees a change, starting build #A-2
12:32 Jenkins A-2 launches #B-2, which runs for the next 80 minutes. A-1 exits out.
13:20 Jenkins job B-1 finishes
13:50 Jenkins job B-2 finishes
--Rob
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