I've just got Kontakt2, and I'm also having trouble with it. I've tried what suggestions there are in this thread, but nothing helps... Basically, after I load the plugin and try to send events to it, it gets set to Bypass (as described before). However, clicking any of the "Stop" buttons kills mpt entirely - I have to terminate the process!
I can quite happily bring up the plugin interface and fiddle with it, though. But using the plugin's keyboard also doesn't work. =(
I've tried loading Kontakt up in another VST host that I have (the pretty dodgy and useless CM Studio), and it flat out refuses to register it.