If the toolbar and left pane are loading, the scripts must be
working correctly. Do you have a way to view a list of the files
that are actually on the server and verify that all your HTML
topics are present?
The reason I ask is that I had trouble recently with one
project in which I was getting application (Java "FileNotFound")
errors in my topic pane when accessing the help through the
application. I use version control, however, and once I had deleted
my files from the repository and then checked them in again, the
problem seemed to be fixed. But if you are doing FTP directly to
the server, you are probably not dealing with application builds.
In any case, the problem appeared to be that the server was not
recognizing that the files were actually there.