Well, all I can suggest is:
1) Put all your settings up to max in the general setup; and
2) Double check you have up to date drivers; if not download them.
If neither of these work, then it could be two things I can think of:
i) the card you are using is too new for the game, or if it is a laptop then laptops are possibly notorious for not handling 3d gfx, as onboard gfx cards imho, are normally screwed; and
ii) I believe the normal thing to do before installing the mods or any mods, is run
BG2 config first, though I don't think it makes any difference.
Personally, I seriously doubt I'm right about i) simply because I'm running a XFX NVidia GeForce NX6800XT myself, and the 3d testing doesn't flicker at all when I run the gfx tests.
So maybe if you're trying a res above 800x600 in the
BG2 config,
ie an unsupported one, try dropping it back to 800x600.
Alternatively, check your gfx card refresh rates under Windows Display control panel.
You didn't say what version of Windows you're running, if it's
XP, you should be able to do this easily, if you are also running
XP and trying to install the opengl software that's on the
BG2 game, that I think refers you to a website,
don't because the opengl stuff was designed for win98 mabe win2k and earlier.
XP handles it just fine without.
If you're using Win98, and you're installing or installed the opengl stuff, that maybe the prob, simply because if your gfx card is fairly new on the market, firstly, no opengl drivers may have been written for it, and secondly, they may never be written because companies tend to write the makority of stuff for
xp these days

If I haven't helped one bit, sorry

But I tried