Suggestion for bug fix
When getting cached messages, in multisites, if 2 chats have the same ids, the messages appear in both sites.
Code shows in chatroom.cache.apc.inc:
$cache_id = variable_get('chatroom_cache_prefix', 'chatroom_cache_prefix') . '_' . $chat_id;
You should include a salt or some kind of site specific id in the APC var name to be sure it doesn't fetch the wrong drupal site in multisite config.
The 'chatroom_cache_prefix' shall manage this I imagine, but it never gets set. At least set the default value to the global $cookie_domain of the site, this might help.