Just a fast snip i was hunting today:
It might be helpful to you, if
- you use RealUrl
- get the errors after following links to pages what definetely are correct and visible
- the errors shows “mp vars”
Get yourself the ‘realurlmanagement’ extension and list the pages in backend hat are the target of the links with it (use ‘pages’ option in module´s view)
The extension may show you several different paths to your page. Just flush them all and you´re good to go.
I was searching for user errors on a larger system for an hour, and did check the realurl caches at last.
And if you´re here but the above solution is not working for you, check the first obvious thing in your shortcut / linking page:
Did you specify the target page? 
check also this TS if u use multi domains with mount-point of another root page:
to setup of the root page:
config.MP_mapRootPoints = root
#or
#config.MP_mapRootPoints = 1,2,3
#with
config.content_from_pid_allowOutsideDomain=1