I thought that you only needed to add the folders to the libraries in Media Center for extenders to see them. But maybe there's additional settings required?
I'm not sure if this applies, but it did to me when I share media files to Wii, PS2, etc.
I only know the settings with Simple File Sharing disabled.
Make sure you have the correct Sharing and Security settings for the folders you need shared. For Sharing you need the Everyone group with at least Read permission checked. For Security, make sure the Everyone group has at least Read & Execute, List Folder Contents, and Read permissions checked.