The site directory uses v3 of kraken/streams/?game=GAME to populate it’s streams, so if you don’t appear in Kraken, you shouldn’t appear on the site at all, and vice versa. That said, caching issues are not unheard of, so this may be a symptom of a larger problem…
Like george said, I’d really need to see this issue live to provide any more information. I recommend joining the IRC channel (#twitch-api on irc.freenode.org) and pinging me (fugiman) when it happens next.