Canon EOS 5D MII...is it just my camera?

If you think it's a problem, call Canon. But since I own the same to cameras and noticed the same issue, I'll tell you they are one generation a part in development and your 5DMKII is sealed against the environment far more than the 40D. Specifically, all the external ons and seams on the 5D Mark II are sealed with rubber gaskets similar to but not as extensive as the pro-level EOS1DMarkIII. The only environmental seals of that nature on the 40D are the foam seal around the battery/CF compartment covers and the large rubber flaps hiding USB and other adapter ports.