I'd read that Clarke started with the Clinton White House as head of terrorism in '92. The USS Cole was in 2000, and he hadn't been able to get the White House to do anything about terrorism all that time. He wasn't very effective as far as I'm concerned. I think the Bush White House was moving him out so he'd resign and they wouldn't have to fire him.
Note they weren't going to move him before October. He was just mad they wouldn't let him brief the president.