It all sounds as if DOSBox isn't set up correctly. Have you had a look at some of the threads yet? There's this one for example:
http://www.abandonia.com/forum/index.php?showtopic=6134
Also, have you checked whether there might be a folder within the game folder? The game folder has to be located in the CDrive folder of DOSBox, otherwise it won't work. (So it has to be C
ARKSEED rather than C
ARKSEED/DARKSEED, if you see what I mean). Sometimes an additional folder is created when you unzip a game.