Are you sure you have "Store full paths" checked? Rebuild them and insure you are packing the parent directory, ie if your stuff is in a modules folder, you need to pack from the parent directory of the modules folder, just like you pack from the parent directory of the art folder normally.
In my experience the cause of packing not working are always:
1)Trying to compress
2)Trying to pack from the folder itself, rather from the parent folder (ie when you pack the art folder, you need to pack from the folder that holds the art folder, so that the whole art folder is packed)
3)Not selecting the "Store Full Paths" checkbox