It sounds as if more than one keyboard is assigned to one manual in GO. Try right-click on one of the manuals. The window below should open. Click on "New", then choose in the dropdown-menu "Event-No" the old entry and delete it. The same with your other manual. Confirm with OK and try. The manuals should have no connection to your keyboards.
After this again right-click on one manual, then "Listen for Event" and push on of the keys of the right keyboard and confirm with OK. The same again with the other keyboard an Pedal.
Does it work?