I'm kinda lost as to why this is. I've had one other person mention this as well. I have all my repository fixes in the CEP Extras folder since they pretty much do the same thing. Everything shows for me. MissPiggi's recolors as well as my own test one I used when creating this. I leave all MissPiggi recolors out at first since there are so many =).
So Vista/W7 has some permission issues with accessing some folders in Program Files, and if you placed them in the bins folder there could be an issue. But the CEP Extras folder is in user Documents where you have full permissions.
So I'm curious as to what your OS is, where you put this, if your CEP is updated, and if you have tried this without any other cc.