It could be that 1080p is only supported in certain modes, or certain games. You might want to ask this question in the MGS subform in the games section. I won't get my LE copy until next week...
I assume your TV is capable of 1080p.
Good ole trickery.
MGS4 has had this problem with people. What was discovered is that ONLY in cutscenes was the game in TRUE 1080p, and during actual gameplay, it was 720p UPSCALED to 1080p to maintain a 30-60fps frame rate.
Plus, the previous MGS games were NOT made in HD.
Let your PS3 and TV chose the best resolution for the game, or stay frustrated and stay in 480.
You wont notice a difference. seriously. i never did until i read up on why MGS4 skips intermittently.