When I upgraded to FC3 (2.6.9-1.667) EVERYTHING (including copying files between partitions etc) was SLOWWW, tried everything to figure out the problem with no success. Yesterday upgraded the kernel to 2.6.9-1.681_FC3 now everything is GOOD.
I am still not sure what was the problem but you might want to try it.
There is a speed penalty associated with SELinux, I think the latest kernel that you mentioned has reduced this penalty. I don't have the link at hand but should not be too hard to find.
Serge