My first bike, about a year after I got it, a trek 1000, creaked when I went up hills standing, or when I was standing. I kept taking it into the bike shop and they couldn't find anything wrong. Finally they flipped the bike over and found a small crack in the frame underneath. The creak was the sound of the aluminum frame pieces rubbing together. Trek replaced the frame for free, which was really great.

Have them check your frame really well.