I ran the textureender on all my texture packs. I then ran Minecraft, and minecraft did not see any resource packs. I checked my %appdata% directory for minecraft. The resource packs directory was empty. There was a new directory called "converted texture packs" I moved the files from it, to the resource packs directory, but minecraft still doesn't see them. If I open the resource packs directory from within, the texture packs are there. They are still zip files, and matching them to the original zip files, they seem exactly alike.
You have done nothing wrong, but there is a conversion tool provided by mojang (texture ender[1]) to convert texture packs to resource packs, don't know exactly how it works, but it seems pretty straight forward.
What have I done wrong?
Sources
[1] http://www.minecraftwiki.net/wiki/Resource_pack