I'm guessing your version is actually 1.1, but is the same version that steam uses.
Steam uses a copy of GTA3 that is version 1.1 without the disk check, while no-cd cracks accomplish this without modifying the rest of the code, R* have remade it by removing a handful of functions, therfor changing some offsets.
We are looking into making a steam/digital download compatible version but it may take some time.
It really sucks how its only 2000 bytes differant (not even that) and it stops us from working with it