We might be having the same issue. What I have noticed is that the Itunes App shows all of my content when I search directly on my Itunes library, on the PC. But when I try to control my Itunes content through an Apple TV, all that I can see is the content that I purchased on the Apple store. Do you see any pattern to the issue?
I submitted a complaint to Apple and someone was working on it, but now it seems she is no longer at Apple.