Wow it's been a while since I've come here. Anyway I know what is causing it and it's actually an outdated engine file. The steam version and the DVD/CD version do not have this problem.
Thank you very much. If you hadn't done this GOG may never have known that they could fix it. I bought this game here 3.5 years ago and it's finally fixed.
I just tested it and I can finally use multisampling and force vsync in the Nvidia control panel without that horrible delay.
We added patch that address this issue. It should appear as 'Universal update' under 'My Account > Painkiller Black'
Thank you, GOG, for following up on this old game.