I figured out how to fix my problem.
To restate the problem again - I originally had to add my Windows shares using the Admin website by following this informative guide - http://wiki.linuxmce.com/index.php/Howto:_Using_Network_Shares
. I could access all of my files doing a search in the orbiter, but they didn't display in the media viewer under Videos, Audio, etc..
After numerous attempts of trying to tweak the shares profiles in device tree on the Admin website, I decide to delete the entire File Server. A few seconds to a minute after I deleted the File Server, my Core system recognized the Windows shares and asked me how to set them up. I selected to use LMCE's file structure. This solve my problem. I did a resync and my files displayed in the media viewer.
I think the problem was that even though I had correctly manually set up the File server and the shares, there was no option to use LMCE's file structure.
Hope this helps anyone that may be experiencing this or similiar problems.