HashMap iterator problem with GATK 3.6 on NA12878 validations

Hi all;
I was running validations with the latest GATK 3.6-0 release and ran into an issue on NA12878 where a region around the centromere on X fails with a HashMap NoSuchElementException. I tried to isolate into a test case and here is a tarball with the smallest set of regions I could reproduce on:

https://s3.amazonaws.com/chapmanb/testcases/gatk36_hashmap_report.tar.gz

This has the inputs and a small shell script to demonstrate.

It's a bit of a confusing one to me. If I try to reduce the test case further -- to only the region that appears to fail when DEBUG is turned on -- it will work. The problem seems to have some dependence on the prior state.

Here is the full traceback:

##### ERROR --
##### ERROR stack trace 
java.util.NoSuchElementException
        at java.util.HashMap$HashIterator.nextNode(HashMap.java:1431)
        at java.util.HashMap$KeyIterator.next(HashMap.java:1453)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.reduceNumberOfAlternativeAllelesBasedOnLikelihoods(HaplotypeCallerGenotypingEngine.java:336)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:264)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:964)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:251)
        at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
        at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
        at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

Any ideas to work around or avoid are welcome. Please let me know if I can provide any other information. Thanks for all the great work on GATK,
Brad