Question: are you accessing your TV shows through the "TV Shows" menu item, or through the "Files" menu item? If it's the Files menu option, then yeah, I can access anything through that, but that's not the best presentation of my media.
In my example, I was seeing my TV shows under TV Shows. I haven't gone through and seen what it is missing, mostly due to how unusable Boxee is on the Apple TV. I really need to give up on the hacky method, and just plop a Mac Mini under the TV again. That would also give me h.264 hardware acceleration if I go back to just using Front Row.
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