Can you send a link where i can see the background problem top investigate the cause.
the remote root and local root settings are taken from your Dreamweaver Site Definition.
The Remote Root is taken from the HTTP Address you set on the Local Info tab.
The Local Root is taken from the URL Prefix you set on the Testing Server Tab.
Make sure the HTTP Address you set on the Local Info tab is correct for your website so that the Menu writer extension can create the Remote Root variable correctly.