ok the game copies the duke3d.cfg file to the home folder so do this first before running the game :
edit duke3d.cfg and set the screen res to 320x240 then run the game.
If you had already ran the duke3d game, delete the duke3d.cfg file from the home folder and make sure the 320x240 duke3d.cfg exists in the same folder as the binary (it will copy it back to the roots home folder).
1) edit duke3d.cfg and set screen res to 320x240 and copy in same folder as duke3d binary
2) rm -f ~/.duke3d/duke3d.cfg
3) run the game