I have had a few problems with the GOG version of Dungeon Keeper gold.

First of all I found that the resolution was low, much lower than I remembered with the original Dungeon Keeper on PC. Turns out that there are no resolution options in the games menu but you can double the resolution by pressing ALT+R.

Secondly I found that the game ran very poorly, in the higher resolution mode. You can fix this by using CTRL+F12 to up the cycles that dosbox is set to initially run at for this game.

Thirdly, when running the game at fullscreen, it stretches to the aspect ratio of my monitor. No matter what I choose when launching graphic mode setup in the game folder. It always stretches. I have tried to fix these problems by editing the dosboxDK.conf file in my game folder. Nothing seems to make a difference. I'm not sure that dosbox is actually looking at this file? As a test I set fullscreen to true and then fullscreen to false. It started in windowed mode both times.

Is it possible that dosbox is reading a different config file somewhere else? The changes that I make by running GOGdosConfig.exe through the "Launch Graphic Mode Setup" shortcut in the game folder don't have any effect on the dosboxDK.conf file.

So what should I do? I can't understand why dosboxDF.conf isn't the right file. It's driving me crazy.

I can't uninstall the game either I get a runtime error when I run unins000.exe

EDIT: Apparently my Intel(R) HD Graphics plugin was stretching dosbox. Or something? I set it to "maintain aspect ratio" and it solved itself. I don't know what is going on.

Try setting it to auto. It also uses dosboxDK_single.conf. You can see this by checking the shortcut. Your A/V software is causing this (false positive).