ls -l /usr/src/linux
and make sure that /usr/src/linux points to the 2.6.9 kernel folder.
If it does, then it sounds like the ati driver is not current. I use nvidia so I'm not sure how ati's drivers are installed.
If it doesn't then
and look for a linux-2.6.9.... directory.
Lastly reset the symlink with
ln -s linux-2.6.9.... linux
Make sure that you work from the /usr/src/linux folder and never from the /usr/src/linux-2.6.9...
Also make sure you complete the linux-2.6.9... with the correct name of the folder in /usr/src/