I was going to say you should have used the spot meter but it looks like you did.
A few points worth thinking about
- Remember the camera meters the scene as 18% grey
- Do you use both focus and exposure lock on the shutter button? If you do then you have probably locked the exposure off the sky. Use custom function 4.3 to move focus to the * button and exposure to the shutter button. This will allow you to focus without locking exposure until the shot is taken.
- Tracking a small fast bird using spot metering (3% of the frame) accurately is going to take a lot of practice.