As of the most recent release, mojoPortal won't create friendly urls that mask physical pages. In previous versions you could avoid the problem by using fully qualified urls when creating menu links to physical pages, ie http://... rather than ~/... or deleting the friendly url using the Url Manager (no need to go directly into the db).
I haven't had problems with the menu myself but it might be worth updating to the newest version and see if it goes away.
I'm getting very close to making a new release, but if you're working with custom code and comfortable building and deploying from source code there is no need to wait for a release, just get the latest from svn branches/2.x
Hope it helps,