Something that really, really annoys me in IPB3.0.x is the way the new PM notification works.
Now don't get me wrong, it's a great pop-up box for short messages, but if a message is very long (for example I've just received a PM this morning from someone that's about 4 pages long if typed in Word), then I get a stupid popup box that's deeper than the screen containing the entire message.
Would it be too much effort to consider truncating the content of the popup box if large messages are received please?