Does anyone else have the problem that DN3D only displays a part of the screen?
I have big, black bars over the game on the right and on the bottom. I have this problem with Unity and also with XFCE when using compiz, so I think compiz is the problem (XFCE without compiz and openbox works fine).

Not sure if this will help with your problem but the following did help for a crash to desktop when dosbox switches to fullscreen on my laptop. Duke3D seems to be quite sensitive about its screen resolution.

Open dosboxDuke3D.conf with your favorite editor with root privileges.

Locate the lines where it says

fullresolution=original
windowresolution=original

and changes those to match your native screen resolution. So if your display is full-hd change those to

fullresolution=1920x1080
windowresolution=1920x1080

Thanks, that did the trick for me :)

I was having problems with Unity and that worked for me too.
Thanks !