I recently set my default padding to three minutes before / three minutes after, and since then I've been finding the system to be more aggressive in terms of marking recordings as watched.
E.g., my wife and I paused the latest ep of Scrubs with just the final post-commercial break stinger left, and when I exited later to watch something else CDVR marked the episode as watched. At that point I was only about 31 minutes into the 36 minute recording (30 min + 3 each before & after).
I tested it, and the cutoff seems to be the scheduled runtime minus about a minute, counted from the start of the file regardless of pre-padding. In a 30-minute show recorded with 5 minutes pre-padding and no padding after, exiting any time after about 29:02 marks it watched, even with ~6 minutes of the actual show left. And of course it getting marke watched means the resume point is lost and it starts over from the beginning.
Seems like this ought to be changed so the threshold is offset by the pre-padding.
These are all recordings from my HDHomerun, with deep processing off and commercial detection off.