I don't have this GOG version (I still have my CD version, when it was called Metal Gear Solid Integral...).
Did you check here , for some tips ....??
All those issues are marked as fixed in the GOG version already and the issue is in the gog version still. Hope this either gets fixed officially or someone in the community fixes it.
Edit: Haven't looked at the widescreen fix because I don't want to artificially stretch the image I'm looking for the original 4:3 with black bars on the sides.