To be fair, Blizzard basically stated after the beta ended that there were balancing issues with Zerg right now and they will be making changes. It's no easy task to balance a game like SC2, so even with the lengthy beta, I'm not surprised there are some issues that still need to be dealt with.
As for other matchups, I'm more hesitant to say there are actual issues since the game is only a week old and it hasn't been put through its paces with high level competition. The metagame hasn't really started to shake itself out yet. We'll have to wait and see what shakes out over the next few months and with any changes to the Zerg matchups.