Well, from what Ive been told, if the Box is in Standby, then it can record three programs at once with padding (because the padding overlaps), whereas if you are watching something, it will only record 2 with padding.
If you have 3 programs set to record, and your using the box, the padding will be removed from ALL recordings, begining and end, even though, come the end of Program one, there is only 2 tuners in use.