I came across this blog post about an issue I had never heard of, but when reading about it I was quite surprised and thought I would check it out.
Lo and behold I could not browse my custom lists from within Office 2013. I implemented the fix as outlined in the post and all was well except for one thing. If I browse up the hierarchy to the site, I would still get e weird view. Is lists all the contents of the site but nothing is clickable. Another click again up the hierarchy to a site NOT using m custom site definition and the view works fine. This implies that not only is there a problem with my list definitions, but my SITE definition as well!
Has anyone ever encountered this? I looked through the onet.xml of other templates but cannot see any differences that might cause this. See top picture for how my site renders in this view, vs the bottom picture of how it should look.