I suspect that the lower clocks the Traytools are reporting are a result of 2D/3D throttling. A GPU will run at lower clocks when there is no 3D applications running, in order to save power and prolong chip life.
I would recommend you get RivaTuner to see what the 2D/3D clocks are and to see about overclocking. I've had great experiences with Rivatuner with multiple cards, including overclocking and unlocking pipes. Unfortunately I can't say how well it works with ATI because I've always had Nvidia. AFAIK it works fine with ATI.