DesktopX has a checkbox under the DX settings/Advanced tab called "Disable system tray support". I use both Litestep, and DesktopX with no problems as long as I have that one checked.

ObjectBar (which also uses Trayserver.exe) has the setting under file/General Options/Startup Options tab. the checkbox is "Disable Trayserver from running at startup" this will similarly make objectbar play nice with Litestep. :)