As you seem to understand, which groups a logical connection (user if you will) is in is something you the application writer is responsible for maintaining across network disconnects/reconnects. If you look at the way JabbR does this, it maintains the state of which "rooms" a user is in in its database. Upon reconnecting, a user's identity helps place the current connection back into the proper set of groups that represent the specific "rooms".
Thanks Drew - I assumed as much, but hoped I was missing the obvious - will grab the jabbr code and look at how they're handing group membership. really is something I feel the documentation would gain from - I suspect it's the pain point of being a (relatively) early adopter though.