Do CBs cover deepest man in the zone regardless of whether the WR leaves the zone now? I could have sworn that I saw some CBs covering WRs even after they left the zone in a few games, but I haven't looked close enough to confirm.

The deep zone tries to stay deep enough so there is no one behind them.

What modifies a CB's decision to stay deep? Is it Zone Coverage? Also, is this in all leagues now or just the Beta leagues?

This was part of the zone coverage updates in 0.4.1. There is a dice roll against a player's zone coverage skill to decide whether they play only players near them or if they are aware of the whole field.

It couldn't have been in 0.4.1 unless it was a fix after the update was released. I remember trying to set up a zone defense right after 0.4.1 was released and getting burned over the top each time because the CB refused to follow a WR out of his zone.

It might have been 0.4.2 (I didn't go and look) but it would have been with the big zone coverage updates. I -might- have tweaked the probability formula in 0.4.2, I don't remember off the top of my head.

Cool. I was actually waiting for this update before trying to create a zone defense again, so now that I know that it should be working this way, I'll build a zone in a few leagues and start doing film review on it again.