I’m developing a theme using a test installation (using InstantWP), but when I upload it to a staging site, for some reason the nav menu looks inflated. After looking at the source, it turned out to be that for some reason my test install uses the class .sub-menu while the staging install uses .children.
Both installs are fresh installs of 3.3.1 with the exact same plugins installed. Why would there be such a discrepancy between the two installs?
What One Trick Pony said; look in Appearance > Menus on both sites and check if the menu has been populated. If so, check to see if the Theme Location has been set and saved. If they are different that may be what’s causing different menu structures to be rendered.
Let us know how it goes – good luck!