Remote Buddy only reads the info from the XML file that's 
automatically generated by iTunes. The Apple TV does not use the XML 
file, but instead streams content and library metadata from iTunes' 
built-in HTTP server. At the end of the day, what you've seen is a 
problem in iTunes itself, not Remote Buddy (and not caused by Remote 
Buddy, either).

By the way: you can rebuild your Library from the XML-file (or an 
edited version of that XML-file):

http://support.apple.com/kb/HT1451

That way, you'll keep your playlists and most metadata intact (except 
IIRC smart playlists).

Best regards, 
Felix Schwarz