I have reproduced the error again:

Job A has been started by manually and executed.

After execution it triggered ((placed to the queue) another 3 build jobs.
At the same time other 5 build jobs have been triggered (placed to the queue) by SCM, 4 of the last 5 jobs are downstream to the first 3 build jobs but one independent (does not have upstream job at all)!

No job except job A has been processed. all other are in the queue for ever.

By the way there are multiple strange log entries in jenkins.err.log like the following

Apr 17, 2015 9:19:45 AM hudson.triggers.SafeTimerTask run
SEVERE: Timer task hudson.model.Queue$MaintainTask@f79885 failed
java.lang.NullPointerException
at jenkins.advancedqueue.sorter.AdvancedQueueSorter$2.compare(AdvancedQueueSorter.java:99)
at jenkins.advancedqueue.sorter.AdvancedQueueSorter$2.compare(AdvancedQueueSorter.java:81)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at jenkins.advancedqueue.sorter.AdvancedQueueSorter.sortBuildableItems(AdvancedQueueSorter.java:81)
at hudson.model.Queue.maintain(Queue.java:1337)
at hudson.model.Queue$MaintainTask.doRun(Queue.java:2435)
at hudson.triggers.SafeTimerTask.run(SafeTimerTask.java:51)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRunAndReset(Unknown Source)
at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

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