Sorry for the late reply, got distracted by life...
I was pretty sure I had it solved at least for my desktop PC, but now have the exact same problem again.
I got myself a new GPU (still AMD) and reinstalled BG as well as the Widescreen Mod. In the CCC, GPU-Scaling is activated and set to "Scale to Fullscreen" (or something like that). But I just noticed something strange: If I start BG (with 3D acc on, so it doesn't scale) and then Alt+Tab to the CCC, the scaling-mode is set to centered and then jumps back to my original selection. So all in all it seems to be pretty weird...
And, as before, if 3D acceleration is activated (like in the imps screenshot above) it doesn't scale but if it is off it does scale exactly like I want it to.
@ Bryll: Yeah, the Imp is right. I want to be able to read stuff comfortably which works pretty well with upscaling. Could you reproduce my problem? And if yes, did you find a solution?