Hi! I don't use that app anymore, but I made a test. I cannot reproduce the exact same bug now, but things are actually worse on gnome-shell 3.8.4-5. The icon is now displayed as a quarter of a larger gray square. There is no tooltip when hovering over with the cursor and the context menu doesn't work at all.
My Java version is currently openjdk-7-jre: 7u21-2.3.9-5. There are no issues in the GNOME flashback mode. Regards Rafał
