When manually adding internal Intranet links in Menu Builder use relative URLs, as opposed to absolute links (difference explained).

For example, instead of using

http://www.mydomain.com/intranet/documents/567

simply use

/intranet/documents/567

taking the address only from "/intranet". This is to ensure that links don't break should you change the domain name of the Intranet, or if there are multiple domain names used for accessing it.