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I observe the same problem without involvement of SCM-polling jobs.
In my case, I have a job A that uses a system Groovy script internally to queue runs of job B (with different parameters). Then job A has a post-build step to trigger job C, which depends on the results of the queued runs of B. Instead, I observe that job C runs immediately after A, "jumping the queue" of all the runs for job B.
The build trigger functions should always place the new run in priority order (if specified) in the run queue, unless "Block until..." is checked.