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mmm, actually I hope you still don't have that problem. You can actually still get messages to pop up. The "bug" arises when you're navigating the site and the notification shows up; then it's as though it prevents the IM console from receiving the prompt to make the message pop up. But if you hit Refresh on the console (or refresh it), the chat window does pop up.

Essentially, once you've stopped navigating the site, if you "Refresh" the IM console, chat messages will ALWAYS pop up. It's just that the IM notification system is like a "first defence" that blocks the signal from getting through.

Also, I'm not 100% sure about the following, but I think that any messages sent after you get the "notification" and before you start navigating the site again will pop up, albeit after a delay, because my impression is that the notification system is faster.