Yes, if the stations you don't prefer are not in your channel list, then the season passes will not record on those channels.Select to record a show on the channel you prefer. Once it is set up for recording, click on the show and choose get season pass. It should then choose the correct channel.
Another thing to try is to remove the 720p channels from your preferred channel list. I believe the TIVO will choose from the preferred list first, but I am not positive on that one.