Hi Adeaphon,
I have the same problem you encountered and I'm trying to solve it getting some info from forums and googling around. I'll tell you what I got by now. First of all the specs of my laptop and the description of the problem so we know what are we talking about: Sony Vaio Pro 13 (SVP1322C5E)
Intel HD Graphics 5000 (no additional graphic card)
Resolution 1920x1080
(others available are 1280x1024 and 1024x768) I first encountered your problem with the fully mod "Baldur's Gate Trilogy" I got from GOG following this guide on GOG.com website. I thought it was something related to the various mods (like the widescreen mod you were talking about) so I tested if I was getting the same problem since the beginning and this is the case actually. I did a fresh install of both "Baldur's Gate - The Original Saga" (v1.3.5521) and Baldur's Gate 2 (v2.5.26498), the last versions downloaded from GOG.com. I describe you the behavior of those two fresh install. Baldur's Gate - The Original Saga: game works full screen, image seems a bit stretched (probably adapting the game resolution to my screen resolution), resolution is 640x480 as you can see from the image below. The game is playable, no strange behavior, no flickering of the image or of the hand cursor (I'll come to this later).
Baldur's Gate 2 Complete: using BGconfig.exe I set up the "Display" section and the "2D & 3D Options" section as you can see from the images below. I enable "Use 3D Acceleration". When I apply those settings I'm asked about performing the usual test where I already notice the problem: the 3 rectangles (red, green and blue) are in the middle of the screen surrounded by black bands. Those have the right dimension and I see them shrinking if I select 800x600 or 640x480 game resolution. I tried to do some snapshots of those tests, but every time I get a screenshot of my desktop area underlying the rectangles. I don't know if this can be a problem yet or if it has something to do with the OpenGL window test.
The game in this case is playable but just too small: I get the 1024x768 game resolution at the center of my 1920x1080 desktop resolution so without any stretching, no fullscreen. I made a snapshot of the in-game image but what I get is only the game area (the OpenGL area?) without the big black borders I usually see. The resolution of this image is 1024x768 as expected (see below).
This is with the "Use 3D Acceleration" option turned ON; if I turn it OFF I get the correct full screen behavior of the rectangles. Playing the game the game image get stretched and so deformed (I think this is my graphic card acting now and it wasn't doing anything before). The game is hardly playable because the hand cursor is flickering and sometimes pieces of my desktop appear on top of the game image. I took a snapshot but again this one looks good, 1024x768 resolution, no stretching, no artifacts. So it seems now that without 3D acceleration my graphic card is stretching the OpenGL image correctly but now producing those artifacts. I think I should stop now with my tests, without applying any mod and try to solve this problem first. This is the fundamental issue. Hope this description will be helpful for you all to understand my (our) problem and to try to find all together a solution. Thank you for reading, bye!