Well, I left out the part where my server runs MineOS Crux.. So my problem may be unique to me.
MineOS is weird, and runs the server out of one directory, we'll call this directory A, and keeps the world data, plugins, mods and other crap in another (directory .. its odd but there you go.
The problem was that I had the config files in only one of the directories. It makes no sense to me at all, but when I put the config files in both directories, it worked.
I'm now playing on a flawless tekkit server of my own creation :D