If the system tray is moveable in that theme, it's possible that the coords got borked and the tray is sitting offscreen somewhere. Does the tray module (systray/vtray/xtray/etc.) show up in the loaded module list in the about box (!about)? A program like winExplorer will show you the size and position of all created windows, even if they're not visible on the screen. You can also use it to reposition the tray window.