Ugh. It didn't make a difference. AHA!! Yes it did. I modified my original zip uninstall the first time accidentally. So even if the folders are the same, it must use the original install path in order to work.
To make this more clear... If you use ridirects, junctions, mapped drive folders etc... in your path you MUST use the exact same path it was originally installed too. Even though c:\Program Files (x86)\Games\Steam\SteamApps\common\Skyrim and d:\Games\Steam\SteamApps\common\Skyrim are actually the same folder (on my computer), the path used in the ModOrganizer.ini file must be the same as the original install path.
