That's not a problem, that's expected behavior for this device. It defaults to landscape for a lot of things and there's no certain way to fix it. Some people have some success by using alternative launchers (go, Launcher Pro, ADW, etc) ... but those don't work for me.
And this isn't a very active forum - I'm usually the only one who replies, and I hadn't checked posts in a fewdays so...
Atrix 2: Rooted, not yet ROM'd.