i had the same problem, i just adjusted the recordings to add a few mins to the end of the programs.
It's not so much the guide info is off but the networks not exactly starting and stopping right at the hour. This is true of Heroes. If you don't have HD for locals, as I don't, and DVR Heroes and CSI Miami OTA, it won't matter what you put for adding minutes to Heroes...it ain't gonna happen.
I didn't do the poll but I subscribe to locals so I can setup the DVR through the guide, especially for New Episodes. You can't setup manually New Epsiodes only.