I do not know if this is a problem with Nexus Dock or the application itself. I have at least 2 applications that do not respond to rigjht-clicks on their system tray icons on the dock. They do respond when right-clicking on the system tray icon of the Windows taskbar. The applications are Free Download Manager and 360 Total Security. Any help is greatly appreciated.

My guess is that those two applications are not responding to right clicks in a standard way. The system tray in Nexus is independent from the real Windows systray (kind of emulates it) and therefore 'passes through' mouse clicks to the applications themselves in a standard way.

Not having access to the actual Windows code that deals with the Windows systray, Nexus reverse-engineered the systray behavior, and might therefore be doing something slightly different from what Windows does - something which those applications rely on.

Left clicking those icons works normally, right?

Left-click Free Download Manager icon works correctly (brings up the GUI). Left-click 360 Total Security icon has no effect (it should also open the GUI). In this case, I just run the executable again in order to see the interface. It's no show stopper. Thanks for all your hard work on Nexus Dock. It's awesome!