We'll create fresh WordPress site with Relative Menu Item Plugin installed. You have 20 minutes to test the plugin after that site we'll be deleted.
Create custom menu items with links relative to the root url of the current wordpress installation.
Simply add a custom link as normal with the url prefixed by %ROOT%. e.g. to get http://mydomain.com/wp/myCustomPage if your wordpress lives at http://mydomain.com/wp then you just write %ROOT%/myCustomPage for your link url.
Create custom menu items with links relative to the wordpress root url.
Not tested with multisite installations.