1. Download files from this directory:
/net/maccoss/vol6/home/nicksh/bugs/brookh_import_nre
2. Open 56_prot_updown_13CL_lable.sky
Skyline will start to import Chromatograms from 2013_Apr_01_RedTide_QEx_52.mzXML and just before it gets to the end, you will hit a NullReferenceException:

System.NullReferenceException: Object reference not set to an instance of an object.
   at pwiz.Skyline.Model.Results.Scoring.TransitionPeakDataPair`1.<GetMatchingReferencePairs>d__0.MoveNext() in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\Scoring\MQuestFeatureCalc.cs:line 759
   at pwiz.Skyline.Model.Results.Scoring.MQuestReferenceCrossCorrelations..ctor(IEnumerable`1 tranGroupPeakDatas) in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\Scoring\MQuestFeatureCalc.cs:line 639
   at pwiz.Skyline.Model.Results.Scoring.MQuestWeightedReferenceCalc.Calculate(PeakScoringContext context, IPeptidePeakData`1 summaryPeakData) in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\Scoring\MQuestFeatureCalc.cs:line 495
   at pwiz.Skyline.Model.Results.Scoring.DetailedPeakFeatureCalculator.Calculate(PeakScoringContext context, IPeptidePeakData peakGroupData) in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\Scoring\IPeakScoringModel.cs:line 325
   at pwiz.Skyline.Model.Results.PeptideChromDataPeakList.ScorePeptideSets(IList`1 detailFeatureCalculators, SrmDocument document) in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 812
   at pwiz.Skyline.Model.Results.PeptideChromDataSets.PickChromatogramPeaks() in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 143
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.WriteLoop(Int32 currentFileIndex, Boolean primeThread) in C:\Users\nicksh\svn\sky_bugfix\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 922

Fixed with r5565

Verified