Place virtual mouse widget on the screen. Configure it to click + left button. Back to play mode and press it. You can test this way right click as well. What happens?
Best for testing physical mouse is warcraft 2 or command and conquer 1. If possible try these games what happens. If these games works then you have wrong setup in duke. In warcraft 2 you can test left click, left mouse down for selection and right click for deselection.
If you hide cursor with mouse wheel or widget then it works like physical mouse on desktop pc. Nobody reported problems. If there is problem, I like to fix it.