I would be able to connect to the 'site', and view the files and sub-directories that existed in the 'Initial' directory, but was unable to navigate into any of the sub-directories.

After e-mailing back and forth with a freind who had similar issues, he told me of a solution that worked for him.

Let's assume that my sites exist in a directory named 'myStuff'. I copied & pasted 'myStuff' into the same directory, creating a 'copy of myStuff' directory. I deleted 'myStuff' and then renamed 'copy of myStuff' to 'myStuff'.

For some reason, this worked...though I am not sure exactly why.