They say it's to put in more commercials and not to disrupt TiVo. CNN had a story about it a while back. They didn't believe it either.
TNT runs back-to-back episodes of Law and Order so that the credits for one episode run at the bottom of the screen during the opening scene of the next one. Since they run the same episode two days in a row, it seems unlikely that this is actually a nefarious plot to screw with TiVo. So at least part of the motivation must come from fitting in more commercials.
A number of networks have stopped airing commercials between the end of one show and the beginning of the next. (As opposed to a few years ago, when it was standard to take commercial breaks both before AND after the end credits). Apparently the networks found that this 5-minute break trained their viewers to flip to another station, and viewers that have seen part of a show are more likely to return to that station.
So mangling minutes in the schedule allows for more ads, higher viewer retention, and screws with TiVo, to boot. Why wouldn't a network do it?