The game has some wierd behaviour on my machine ( specs detailed at the end of the message ).

The desktop shortcut seems to ignore the dosboxDK.conf file settings, even when I DELETE the conf file its still the same. Plays reasonably but has the black bar across the bottom of the screen, really annoying.
I tried the suggestions in the forums re tweaking the conf file but the desktop shortcut just ignores all the changes.

The graphic config exe changes the game when run from the config tool but the behaviour of the game is strange, it either goes full screen with a tiny game in the middle , or has 2 black bands on the sides and the audio stutters , or works well in low graphic mode but goes small and jumps around when I press ALT-R.
The OpenGL , OpenGLnb , Direct3D options cause it to get stuck in a black screen I need to task manager kill the application.
The game seems to ignore aspect settings and scale options.... best I got was big screen with 2 large black bars on the sides but then the audio stuttered badly, especially after the level.

Machine specs are:
AMD Athlon II x4 630 (OC'd to 3.4 ghz) , 4 gigs DDR3 ram , GTX580 graphics card and a ExtremeGamer X-Fi sound card.
OS : Win 7 64 bit Home Premium ed.
Drivers up to date, and PC is properly maintained.

I think you're editing the wrong file. Simply put: there's no way the game would start without a config file, since the instruction to actually start the game is, you guessed it, part of the config file.

There are three files:
dosboxDK_server.conf
dosboxDK_client.conf
dosboxDK.conf

The last one (dosboxDK.conf) is the one that's used for a normal game.

I checked and that was the file I was changing, it just seems that the desktop shortcut isnt using the config at all despite the command line parameters telling it to.
The graphics config program does change that file, and when you run from the config program it uses the changes... but the desktop shortcut doesnt.
I even right-click - open file location... same install area.

I have even DELETED the conf file , and the shortcut launches as normal.

this is the shortcuts command line : "C:\**********\GOG.com\Dungeon Keeper\DOSBOX\DOSBox.exe" -conf dosboxDK.conf -noconsole -c "exit"