PokerTracker

Even though the box is checked no stats appear or are stored for viewed tables.
On tables I'm at, they only store stats when I'm actually playing, not when I'm sitting out or waiting to play.
Why is this?

What site are you playing at?
Not many sites write hand histories for observed tables.
I suspect that you're talking about Full Tilt? They do not allow datamining and no longer write observed hand histories. The new Memory Grabber option will read hands but NOT import them so the only stats shown are those already in your database.

I play in ipoker.

iPoker does not write hand histories for observed tables so there is nothing for PT3 to import (unless you buy a handgrabber - do a web search for "ipoker handgrabber" and you'll find plenty of options).