See Test-1

What happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name

#Data used
chr1 30427671
chr2 19698289
chr3 24459830
chr4 18585056
chr5 26975502
chrC 154478
chrM 366924

note: chr3 different size

Result:
Difficult to repeat has to do possibly with starting from initial load having one load before the other or order of appearance in "Data Sources" list

WARNING: Found a feature with null style
Mar 06, 2014 5:10:06 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
INFO: Loaded TAIR10 mRNA in 4.199 secs
Mar 06, 2014 5:10:09 PM com.affymetrix.igb.view.load.GeneralLoadUtils$3 runInBackground
INFO: Loaded TAIR10 mRNA in 0.001 secs
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at sun.security.provider.DigestBase.engineUpdate(DigestBase.java:127)
at java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:568)
at java.security.MessageDigest.update(MessageDigest.java:323)
at java.security.MessageDigest.digest(MessageDigest.java:398)
at com.affymetrix.genometryImpl.util.UrlToFileName.toMd5(UrlToFileName.java:107)
at com.affymetrix.genometryImpl.util.PreferenceUtils.shortNodeName(PreferenceUtils.java:636)
at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:657)
at com.affymetrix.genometryImpl.util.PreferenceUtils.getSubnode(PreferenceUtils.java:650)
at com.affymetrix.igb.tiers.TrackStyle.<init>(TrackStyle.java:139)
at com.affymetrix.igb.tiers.IGBStateProvider.getAnnotStyle(IGBStateProvider.java:61)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.setStyle(QuickLoadSymLoader.java:207)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:146)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:129)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:109)
at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:354)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:941)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.loadOnSequence(GeneralLoadUtils.java:847)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.access$400(GeneralLoadUtils.java:713)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3$3.run(GeneralLoadUtils.java:788)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)