No problem! I have never had that happen so I dont know how to fix it. Just to make sure, are you changing the files in the Mods folder or in the game directory?
Make a folder called mods in your gta folder, then take the files you need to replace such as Update folder, x64 folder, and the .RPF files and copy them in the mods folder.
Make a folder called mods in your gta folder, then take the files you need to replace such as Update folder, x64 folder, and the .RPF files and copy them in the mods folder.