I keep getting this god damn error.

---START PATCHING---

[OFFSET PATCH]
loading file:
C:\Program Files (x86)\Steam\steamapps\common\Prototype\prototypeen ginef.dll
Wrong filesize or already patched!
nothing patched!
...done!

---PATCHING DONE---


Does this just not work with the Steam version or am I doing something wrong?

Did you try running patch as admin?
Game is located in "C:\Program Files (x86)"

Still crashing when loading save game or new game.