Ok, I had this same problem when I was trying to install it on 1.6.4, but I can't remember how I fixed it. I installed NEI correctly and installed CodeChickenCore with it. When I load up my Minecraft, neither mods show up on the mods list, and they won't activate in game. I have uninstalled and reinstalled, used a mod installer, everything, and I can't get it to work. I tried to install Waila and I got a message saying that NEI wasn't installed. All that I can guess is that Minecraft simply isn't detecting the mods, which is odd, as CCC and NEI are the only mods it ever has this problem with on my computer. Any suggestions?
And yes, I deleted the META-INF files.