I have added your settings on the expert mode and I dont see much of a change. By Game Tuner you mean the Game Launcher? i have the highest setting selected globally (prioritize performance)
Maybe it has to do with the fact that this version of Duke 3d is asking for my .iso? im playing with the iso loaded, otherwise it doesnt let me play as it ask for the cd… weird. I have another duke3d.exe on my computer that doesnt ask for a cd, or maybe its because its not playing in dos mode? im not sure. Its the Atomic Edition. Can you test episode 4 level 1? its specially slow there.
Also when I look at sprites like the fire animation, i can feel the lag. In episode 1 level 1, the fire sprite on the trash for instance.
My 800×600 performance is an slideshow compared to your video.