Victor is right
Good point Victor - this fixes the problem for me after I make edits by hand or through the wizard. I do not auto enable uploading related files so have to remember to send the related js files manually.
DW CS4 makes this so much easier where it shows you the related files across the top of the page - click the file to see the source code (if in Split View) then Ctrl-Shift-U to send that particular file to the server. THis has been saving me loads of time hunting down related files, then opening, editing, and uploading them individually.