Tell me about it! Its trying my patience. When I send group notices or anything but chat, the active window will switch to the main chat. When I win this battle I'll report back. All I can suggest for now is don't press enter or look away from the screen. Lol, just be aware for now where your text is appearing. I find it will switch every 20 seconds.
...update: ok i found it, in preferences, chat, choose "flash toolbar button" on everything, it should now just flash orange, and not steal the mouse.