Try this as this is something I suffered with too... I thought the css menus had broken; look in the wa_settings table of the database and there you will see something like:
Root URL: www.sitename.com/
Local Root: /
Remote Root: /
You need to change the above to:
Root URL: sitename/
Local Root: /username/sitename/
Remote Root: /username/sitename/
I think I have that the right way around for your purpose. I did it the other way around to you, I installed locally, then ftp'ed to the remote server. If this doesn't work straight away for you switch it around, or you could do a test install with a test db, then get the info from wa_settings that way. But, as far as I am concerned, it should work if you make these changes.
The only thing that might not work is the logo's on the pages as for some reason my remote install has:
whereas my local install has:
If you get this working so both local and remote have the same code, I'd love to know how you did it.