Do you have channels hidden on ATV2? I have both 2 and 3 and they get the same channels, just not at the same HDTV quality (1080 on 3 vs 720 on 2). Do you have automatic updates enabled?
To check for updates on ATV2, Settings > General > System Updates > Automatically Update, then for good measure Update Now (top item)
To check for hidden channels, Settings > Main Menu > Toggle Hide to Show for the channels you want to see or vice versa.
I did this from memory so titles might be a bit off, but you'll get the point.