Did you remember to take your filters off your lenses? haha =]
Many cameras take a center weighted reading that sometimes includes a larger part of the bottom of the frame than the top. Intended to give a bit more emphasis on the immediate foreground than the sky kind idea, this may be the difference between using your hand held meter which just calculates everything all evenly.
Time to get a spot meter (they are great btw), or just dont worry. =]