So THAT'S what I did wrong! I can't believe I did that, I've looked at some of the topics already on here which suggest that you start the game before patching it. Man I feel like a moron, lol.
From the way you worded it, it sounds like you installed the game, and then patched it without starting it. This will cause problems, since the patch needs the game's ini file in order to install correctly, which isn't created until you launch the game for the first time (in administrator mode, if you're on Vista, 7, or presumably 8).
Thanks a ton program! (I mean it)
Umm, actually, running the game before patching is completely unnecessary. The patch isn't looking for any .ini (actually .cfg) files to modify. Whatever problem has been occurring, it had nothing to do with that.
Now, if you want to install the Killer App Mod, different story. Yes, the mod needs to modify a .cfg file that won't be there unless you run the game at least once. And you definitely want to be running the game with Administrator privileges from the start, or else it will never save your preferences in the game and cause all kinds of problems.
The next version of the mod (due out in the next 2-3 months, hopefully) is going to make installing and patching the game much less of a headache than it is now, because it's going to incorporate the patch into it, automatically set the game to run as Administrator (so you don't have to do it yourself), along with a lot of other improvements.
But right now the patch and the mod are two different things.