This Apple support document, I believe, holds the key to an issue I've been having with the Apple TV lately:
There are two ways to get iTunes content from your computer to Apple TV—pairing and sharing. This document explains the differences between pairing and sharing on Apple TV.
iTunes automatically syncs content, giving priority to newer items. Items that are not synced are automatically available for streaming when iTunes is opened.
iTunes streams content to Apple TV. Content is not stored locally on Apple TV.
Note: Paired computer content appears in all Apple TV menus that start with "My" while shared computer content appears in all Apple TV menus that start with "Shared."
Fair enough. But here's the thing. When I first updated the Apple TV to the 2.0 software, I am positive that I could both pair and share, which I took as a major advance. That is, I paired the Apple TV with my PC-based iTunes collection, and synced whatever content to it. If iTunes was off, the Apple TV would of course present whatever content was on the device. But if iTunes was on, I would also see the entire contents of my PC-based iTunes collection. It was the best of both worlds.
I can't get it to do that any more. Am I missing something?
UPDATE: Thanks to François S. for what looks like the solution. I'll try this today:
I had the same problem as you with my AppleTV. There are two ways you can fix this. Either set syncing to "Automatic Sync", or make sure that the "Show only the..." checkbox is unticked if you choose "Custom Sync".
I prefer the latter as "Automatic Sync" causes iTunes to dump all my music on my AppleTV, while I prefer it to give priority to videos and movies.