Ok, I noticed this quite quickly on Vista, the taskbar button (conversation window) won't flash when I get a message IF the tabbed chats are enabled. Disabling tabs makes it function correctly again. Also, the chat tabs themselves won't flash/blink when I get a message, so I think they're both related to this.

I read from the changelogs that there has been an improved vista support, but maybe some things have been missed. I'm hoping to see this fixed in the next  version, I can't live without tabs