So I wanted to play this with dosbox to get as close as possible to how it felt to play it back in the day, and for the most part everything runs fine except one thing, sometimes the gun models on Duke flicker badly this is also mirrored during the opening where the Atomic Edition logo also flickers real bad. Anyone have any idea what could be causing this?

Enter the game folder and open dosboxDuke3D.conf with any text editor.
Look for the [dosbox] section: you have to change the machine variable. Try setting "machine=vesa_nolfb" or "machine=vesa_oldvbe", then save the file and run the game.

Thanks V "machine=vesa_nolfb" worked just fine. So, the dosbox version just won't run in VGA mode? Granted not seeing much of a difference here.

VESA modes are basically SVGA (256 colors at up to 1600x1200 and full 32- or 24-bit color at up to 1024x768) and they should be backwards compatible with VGA. Anyway if you want to set a true VGA mode (16 colors at 640x480, or 256 colors at 320x200), you have to put "machine=vgaonly" into DOSBox config file.

Thanks. Setting machine to machine=vesa_nolfb fixed the problem for me as well

It worked for me too, thank you.