Magic_Of_Light: The thing that is making this so hard, and I have like no choice but to edit the config file here it seems, is that the dosbox config files are no longer easy, they are a wall of text, making you strain your eyes to keep track of things and find the things you need to edit.
Do you mean the formatting of the config file is wrong, as if all the text is on one long (wrapped) line?
I think GOG's DOSBox setup tool replaces the linefeeds in the text with unix-type linefeeds, which e.g. Windows Notepad doesn't identify (hence, Notepad doesn't know where a new line starts, but shows everything in one line).
If this is the problem, open the config (text) file with Wordpad instead, it should display it correctly. After you save it with Wordpad, you can also see it ok with Notepad (ie. Wordpad seems to save it with Windows linefeeds).
SirPrimalform: Try ddraw with normal3x as the scaler. The scaler is applied first, so a 320x240 game becomes 960x720 and is then scaled up the rest of the way with the bilinear filtering you're complaining about. Very different from just going straight from 320x240 to 1152x864 with bilinear filtering.
I was under the impression that if you use any of the scalers, then the windowresolution setting is disregarded, and e.g. a 3x scaler would only give me a 960x600 window, which is vertically too small for my 1600x900 screen. Maybe I was wrong then.
I'll experiment with it. My main priority is to get the game window to the correct size, and then worry about if the pixels are exactly square or whatever. As long as they are not as badly distorted as in stretching e.g. a 4:3 image to 16:9, that I don't like.
EDIT: Ok I set it now to ddraw with normal3x, and leaving the windowresolution to 1152x864. I seem to still get the correct window size so I guess this is fine then. I can't tell if the graphics are any better (or worse) than before, same blockiness as 320x200 DOS games normally are to my eyes. :) I experimented it with TES Arena.