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, a