I have a similar problem and have given up trying to fix it. I think I've tried every poorly written "HOWTO FIX GTA4 GRAFIX" guide on the internet.
I tried contacting Take 2 support about it. I dropped them an email explaining exactly what the problem was, even gave them links to forum threads by other people having the same issue and despite them saying I'll hear back within 72 hours, I haven't. And that was probably over a week ago now.
I'ma ring 'em when I have time to, but I doubt they'll be able to fix it over the phone. Gonna need another patch me thinks.