Actually you don't need to download my patch at all. Skarok merely states that his campaign uses the settings and balance created from my patch, but all of the configurations are limited to the levels you apply it to. You can download Skarok's campaign and just play it as it'll already have the patch applied to it, and it won't effect any other part of the game.
I have the same problem, actually. It's weird, because I never had that problem with my 1.3 folder, but after installing the General Improvement Mod, I began getting that issue. I don't know why. Try removing that folder or something. I can't guarantee a fix though, as I haven't tried it myself.