Many thanks for the beers! Very much appreciated!
I'm not entirely clear what you mean by the mojoportal menu. Are you talking about the main site menu, the administration and edit links? Can you clarify.
If you're still logged in as admin I would check the system log to see if any related errors might be getting logged. Even if the admin links are not showing as long as you are logged in as admin you should be able to navigate directly to /Admin/ServerLog.aspx
If you're working from the source code repository I recommend pull the latest changes with Tortosie HG, then do Tortoise hg > update to apply the latest changes to your working copy, then rebuild your solution and visit /Setup/Default.aspx again and see if that resolves it.
Hope that helps,