There are several things at work here, and I don't think the intent is to screw with DVR usage so much as it is to keep eyeballs glued to the present station.
With the remote control becoming ubiquitous about 20 years ago, networks started blurring the ending of one show and the beginning of the next. Previously, they would often run a commercial in between the ending of one show and the start of the next. Now, to keep viewers from channel surfing, they go immediately from one show to the next.
The next thing they tried was a little more insidious. As you noted, TV networks started the having some of their shows run 1 minute long (e.g. Gray's Anatomy). If you then switch to a different network, you'd be 1 minute into the new show, so you'd be more likely to stay on the network you were already watching.
Add onto this a little timing sloppiness on Comcast's part and/or the network feed and you have situations where your DVR recording either fails to get the last 2-5 seconds of the show you were recording (usually the "scenes from next week") or the first few seconds of the show you are trying to record. If I can, I always set my recordings to go 1 minute past the scheduled end, but that's not always possible if there are a lot of shows I'd like to record clustered together.
It's annoying and I think it's just going to accelerate the switching to video on demand or pay-per-episode viewing. I'd use on-demand to watch certain show more frequently (e.g. when there are more than 2 simultaneous broadcasts I'd like to watch) but, since one can't fast-forward through the commercials in on-demand shows, it's a less pleasant experience.
On a slightly related topic, does anyone here know if Comcast has any plans to introduce a new generation of DVR equipment? Our old 6120 unit has pitiful storage capability by 2012 standards and the software running the system still looks as if it were written by a summer intern.