Passed V.13686, Mac, Java 1.7.0_09
Hiral was correct about dragging in the link.
Files were downloaded and dragged in from Desktop for testing.
Selecting two graphs and using any 'Single-Graph' option in the 'Operations' Panel of the 'Graph' Tab will produce two new graph tracks that display the proper results of the selected operation. No blank tracks appear in the main viewer and no exceptions/errors are visible in the java console.
There was no issue with loading data in chr1 vs. chr21. With the attached files, no data loaded in chr1 but did load in chr21.
fixed by Hiral in rev 11771.