I don't know why, but when you initiate DoublePlay, it does not automatically go to the last channel you watched. Instead, on my DVR at least, it always goes to WGBH which is 2-1. I think if yours goes to 3, that means it must go to the lowest available channel. But what's to stop you from changing channels? The whole idea is that you can change either channel independently. When you initiate DoublPlay, if it takes you to a channel you don't want, just change the channel. You will still go back to the initial channel with the next down button press.
So in your case, you would be watching channel 8. You hit the down arrow twice, and it brings you to channel 3. Press the channel up button to get to channel 5, and now if you hit the down arrow, it will toggle between 8 and 5.
I don't know any way to stop it, but I don't think there is a need to until the second tuner needs to record something. At that point you will be given the options of recording or continuing DoublePlay.