(Note: this visual is a very rough approximation of relative sizes of spot-meter spots for the purpose of illustrating my point. And, in fact, the spots are circles, not rectangles. But I couldn't spend all day on this.)
Canon is infamous for its overlarge spot-meter circle sizes, and the 40D's has increased over the 30D--up to 3.8 percent of the viewfinder, the same as the 1D Mark III. In contrast, the Nikon D80 uses a 2.5 percent spot size.
The spot circle size matters for photos like this, where the area you want to meter off is small and proximate to an area that would deliver a different result. I was trying to meter off the bird's head, but think the metering circle extended to its more brightly lit shoulder, which caused the underexposure.