- No transparency (only theme background color) when you have the tray icon with new count display enabled.
- Full transparency when you have the tray icon without new count enabled.
So to allow the user to decide how important transparency is, for the configuration variant without new item count rendering, the old code supporting transparency (using a GtkImage widget) is used. And if you absolutely want to see the new item count number you have to live with a non-transparent icon background, which should be ok when you use non-transparent panels. To change the settings have a look at the preferences tab "GUI".
Solution in upcoming 1.2.18 and 1.4-RC1