Try "disabling" the manual feed. You should be able to find this option under the "General Print Settings" menu on the printer. "Disabling the manual feed" option just removes this tray as an automatic tray option when printing. You can still you use the manual feed tray, but you will have to specifically select "Tray 1" or "Tray 1 (Manual Feed). This is how we wanted the printer to function.
Hope that helps. It worked for us.