Ok, that is weird. Everything seems above board, except one thing. In the GameInfo for the mod, you have 895 files. In the GameInfo for the main directory, you have 896. That means there is one less file in the Mod'd folder. This maybe part of the mod, but I doubt it, as I'm pretty sure all mods either change(same number as main directory), or add(higher number than main directory) files, rather than remove.
The one thing to do really, is either find out which file is missing, or, a quicker way, copy all the files in GameInfo from your main directory into the mod's GameInfo folder, and when asked to replace, click 'No' on all(895) of them. One file should be new, so you won't be asked to replace it.
A couple of questions that you may or may not have asked already, but just for clarity, and for me;
- Did you create any of the Folders manually at anytime? (Right clicking, New... -> Folder)
- Is your username user?
Good luck, I'll be back tomorrow lunch (GMT), if you're still stuck, or maybe someone else can help you 'til then.
Edit: @ Carbon016; No, he has done that correctly, check the dates on the files in the main directory's GameInfo folder.