I'm getting really frustrated with the installation, and I feel stupid because it's probably some little mistake I'm making. I'm having several issues. (Steam installation, Windows 7).
First, I have 224 mods in the left pane, not 204. I deleted all mods from the Skryim loading menu, and I uninstalled/reinstalled the game. No change in mod numbers. I'm also having the same issue that zshguru is having, none of the plugins are showing up in the right-hand pane of ModOrganizer. I tried your suggestion, RottenDub, but I can't find the folder you mention. Any other suggestions?