Are these happening on different local Sites (with separate site definitions?)
It is possible that in one site you have the 'Links relative to site root' option selected, and another, the 'Links relative to Document' option selected?
A path that begins with a /forward.slash indicates that it is set to be relative to the site root.
The site root relative path could be being set externally, depending on whether the MenuWriter is being used on its own or in conjunction with another program. Check to see what the 'relative to' setting is in Dreamweaver > Site > Manage Sites > (select your site) > Edit > Local Info > 'Links relative to'.
I would say that if you are building a menu rather than editing one that is incorporated into another solution, that it is better to keep your links relative to 'Document'.
You can also change the setting when you click the little folder to select a link, - it is at the bottom of the folders window that opens up.