TO REPRODUCE: Using clean preferences and clearing the bundle cache start an IGB session. Timing is important here so I will be as detailed as possible. From the welcome screen select Blueberry and wait for tracks to load. As soon as tracks load you should notice that the loading bar in the bottom left is still in an indeterminate state. Quickly open a bed file (the one attached to this issue) The file will start to load and then IGB will start throwing many java.lang.NumberFormatExceptions

here is the last one on the list of many

java.lang.NumberFormatException: For input string: "+"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:484)
at java.lang.Integer.parseInt(Integer.java:527)
at org.broad.tribble.readers.TabixReader.getIntv(TabixReader.java:274)
at org.broad.tribble.readers.TabixReader.access$300(TabixReader.java:43)
at org.broad.tribble.readers.TabixReader$Iterator.next(TabixReader.java:351)
at org.broad.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:43)
at com.affymetrix.genometryImpl.symloader.BED$2.next(BED.java:255)
at com.affymetrix.genometryImpl.symloader.BED$2.next(BED.java:244)
at com.affymetrix.genometryImpl.symloader.BED.parse(BED.java:211)
at com.affymetrix.genometryImpl.symloader.BED.processLines(BED.java:269)
at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:156)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:276)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:154)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:130)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:110)
at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:354)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:955)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.loadOnSequence(GeneralLoadUtils.java:859)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.access$400(GeneralLoadUtils.java:724)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3$3.run(GeneralLoadUtils.java:800)
at java.util.concurrent.Executors$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)

SUPPLEMENTAL: Seems you can get different outcomes depending on timing of opening the BED file.

If you open the bed file IMMEDIATELY after opening Blueberry IGB forgets that it was looking at Blueberry and opens the BED file as a custom genome.
If you open the bed file AFTER TRACKS have been drawn you get the described errors reported in this current jira issue
If you open the bed file dialog IMMEDIATELY after opening Blueberry but wait for tracks to be loaded you get both outcomes (IGB opens file as custom genome and throws NumberFormat exceptions)