Apple suggests that users who have updated to the 3.0 version should immediately update to version 3.0.1 in order to prevent content from temporarily disappearing until re-syncing.
The Apple TV should be restarted and updated through the "update software" option under the Settings > General menu. If this does not resolve the issue, it is recommended that the Apple TV be disconnected and reconnected to the computer that it is networked with.
A final option if the above actions do not fix the issue is to perform a factory restore, update to 3.0.1, then re-sync.
Apple TV was updated Thursday to version 3.0 which added an entirely redesigned main menu, support for iTunes extras and LP, streaming Internet radio, and Genius Mixes. This was the first major update for Apple TV since early in 2008.