You mentioned that shows end a minute or two late - but do they also start late? (If not then it's not the clock, right?)
You can also compare your time to: timegov.nist.gov
That's the official time, though broadcasters are not obligated to follow it. Broadcasters don't like DVRs. DVR users tend to skip commercials, which annoys the customers of the broadcasters. (Which isn't you - you are "the product" from the broadcaster's perspective.) Heck, some company we've heard of even has a DVR that can automatically hop over them for you.
How annoying do you think that is to the guys who want you to buy their deodorant???
Basically, think of yourself as the fish, trying to eat the bait without getting hooked.