Thanks to Sasza, I know what the bug is xD Silly mistake with the very first channel you put in. I'll edit a bugfix and let you know tonight.
@Firstmate: Yep. I'm working on that too. That's actually a really easy one to write up. :)
As for passwords to channel, just put them in the channel editbox after the channel name.
e.g. #channelwithpassword password
If you add that, it will work.
Quick question for other lurkers, should I bother making a password field for channels? Or just keep it like that (And edit the hover-over help so it actually says to do that.)