Autotune cuts off the last few seconds of what you are watching and jumps to the autotuned program

DTV sends the same time code to all receivers so maybe the programs are off.

I looked at the clock on the TV when it switched and it switched at 6:59 even though it is suppose to be ON TIME.  So it is the software that is doing it.  One minute before is not ON TIME!

well the reason that happens is because the receiver autotunes a couple seconds before the scheduled autotune to prevent the TV watcher from missing the beginning. 

It is actually 30 seconds of the show you are watching that it cuts off to go to the Autotune.  I want to watch/hear the last few 30 seconds of a show I'm watching.  It should be ON TIME, not 30 seconds before or after.  Very Frustrating for me.  sometimes the last few seconds of a show is critical.  The beginning you can usually catch up. 

Alright. Well the only tip I have for you is to record the end of the show so that the auto tune doesn’t ruin anything. But I understand, it can be annoying at times.

I'm guessing you have a Receiver, not a DVR. DVR's can't Autotune. With a DVR you could record both shows and wouldn't miss anything. I can assure you that DirecTV won't be updating the Receiver software to change this behavior.