Conflict between pages and menus ?

Working with the bp-fun theme (although I think the same happens with bp-social) I've been adding some content in pages which then appear (automatically) in the navigation bar along the top, as expected.

I then added the directory plug-in at its own site mysite/directory/ with its own theme.

For my main site to then link to it, I add a custom menu within the bp-fun theme options to display in the main navigation area.

I go to the site, and sure enough, there it is. But all-but the buddypress navigation items have disappeared (ie there are only home, activity, community and directory), all the pages I've added that were previously there have gone.

If I delete the custom menu my pages re-appear in the navigation bar.

So is it one or the other?

Design feature or bug?

Can I have both, please?