Cutting short recordings

Ive got a Hughes/DirectTV DVR Tivo (DVR 40), and it seems that over 90% of the shows I record are cut short by one minute.  It would make sense if the DirectTV master clock was off by one moment or if all the TV networks were producing 31 minute long shows to try to make people see one more set of commercials.

Example.  I have the Daily Show and Colbert Report on to record.  The last minute of the DS shows up on the first minute of the CR.

Example.  I recorded the 400 Blows (famous film).  It missed the famous last shot i n the film.

Example.  I have to set the DVR to add one minute to the end of all my shows or I miss the final punchline or answer to most shows.

DTV says they've never heard of this, or I need to reset my shows higher in priority, but just about EVERYTHING gets cut off and I'd need to figure out what gets cut off by what!

Has anyone seen this before?  There are all sorts of places where this can be triggered from the network all the way to my hardware or the programming, so there's no easy culprit to identify.

Ideas or others suffering from the same problem would be appreciated.