I see in the prefs for the new beta, there is much more control over the Genre tag in that we can use MusicBrainz or Discogs like before but now can set either to use the Genre or Styles of Discogs and in what order.
There is also a preference for how many Genres to set.
Ultimately, how did you implement the multiple Genres? Multiple tags or a delimiter in a Genre tag?
How does iTunes interpret it? (Right now I have the checkbox for “Save Genres in iTunes-friendly format checked”)
Edit: Reading http://www.jthink.net/jaikozforum/posts/list/1291.page
for some insight.