I have had the same problem...I have several folders and a copy of the menu.js and exported files in each folder. Then, I made my paths ../FolderName/filename.htm.
For example, I have a folder named GetStart and within that folder are all of the exported files from Fireworks. My links in the (menu.htm file - the file exported from Fireworks) are ../GetStart/filename.asp.
Hope this helps.