In case anyone is interested, I've been going back and forth with Sony support on this. Tried the official support forums but all that got me was the advice that my PS3 (as well as others reporting the same issue) must be defective.
After a couple of false starts, it seems to come down to the fact that the games are mislabeled on the retail box... at least that is what I am reading into my latest reply quoted below. While they do support and can run in 1080p, their default is actually 720p. Not really surprising as the vast majority of PS3 games are 720p but frustrating when what is on the box is wrong.
Unfortunately, if the game is defaulting to 720p then that is the Native Resolution. As you stated, the only way to get the higher output is to force the system into 1080p at all times. Although, if you put in a game that only supports 720p or lower, it wont play at all. The game developers set their games this way, because the game performs better in the Native Resolution than a higher one. Furthermore, some games will only support the highest resolution during cut scenes, and will use lower resolutions during game play. For more information on a specific game please contact the developer for that game.
The "it won't play at all" part is wrong, they drop down to 480p.