3
I've noticed that some themes (in particular) and modules are packaged differently than others--this could be causing the problem.
For instance, you might download a module in folder "coolmodule" then open that folder and find a folder called "modules" then inside that folder find another "coolmodule" folder. The only module to upload would be the last one. On other occasions the top/main folder called "coolmodule" would need to be uploaded.
I'm not sure if I'm explaining this well--but open the folders that contain the non-working modules and see if something doesn't jump out at you.