So, I've recently set up a virtual DOS machine using DOSBox and a vhdx hard disk image I created with PowerShell through Hyper-V, and I installed a whole bunch of my old games that I had on floppy and CD, including (of course, or why would I be posting here, right?) Duke Nukem 3D Atomic Edition. However, I've hit a bit of a snag, and I don't know how to proceed. Now, initially, I installed Duke3D from my Kill-A-Ton Collection disc set, and applied the Plutonium Pak from there as well, and it required me to use my Atomic Edition disc to play. No big deal. However, when I quit the game, it hangs with a flashing cursor at the bottom of the screen and no DOS prompt. Okay. Maybe something's wrong with my Kill-A-Ton discs. They are getting on in years. I check for pinholes, nothing. I use my bin/cue set I made a few years ago. Same problem; hangs on exit, no prompt. Alright, this time, I use my Atomic disc to install from, thinking maybe I got lucky, and there's some kind of defect in my discs that's press-related. Same issue. What the heck is going on here? Has anyone else encountered this? Duke3D is the only game that I have installed that hangs on exit. Is this just a DOSBox thing? I'm assuming that since ALL of my discs are doing this, it's not my discs after all. If anyone could help, it'd be much appreciated as I'd like to relive the DOS experience without having to shell out a ton for a period machine, though, that would be the ideal thing to do.

Strange...well I bought Duke Nukem 3D Atomic Edition from GOG and it runs damn fine.
Did you try to start the game though a batch containing "exit" at the end? Sometimes this helps...

Yeah, turns out it's a combination of things; After some experimentation, firstly, it turns out that the entire 0.74 line of DOSBox conflicts with the CD version of the game, and secondly, much like Manhattan Project, The GOG release of Duke3D uses a fixed EXE to avoid the CD-ROM bin/cue bloat. The apparent side-effect is that it fixes the hang on exit problem with DOSBox 0.74. Unless the EXE actually addresses the issue or they're running a custom build of 0.74. I'm actually gonna have to test that last thought; would be nice to have the benefits of 0.75 without the issues.
Edit: Also. Turns out that installing on a virtual hard disk has some issues with DOSBox. Just tried a retail install of Duke3D on a loose directory setup, no problems. What the hey lol

Is there any difference when running DosBox-Staging? Just for curiosity's sake.

Not sure. I'll have to check that out. Have to try it with a "hard disk", too. I'll upodate you as soon as I check it out. Also, sorry for the late reply