I would do a thorough CHKDSK on that drive by running chkdsk /r.
Then see if that resolves your issue. If that does not do it, I would recommend you go to the root of that drive and take ownership of it and grant yourself explicit full control rights to it and all subfolders and files and see if that fixes it.
If you still get to folders that show they are empty, but you know they should not be, then do the same thing by taking ownership and giving yourself explicit full control rights to the folder and all subfolders and files.
Thanks for answering, found out about that taking ownership a few minutes ago and it worked. Thanks for confirming that in your post
- Have a wonderful 2013!!!