Not sure if this is the correct place to post this, as I did see this in 22d rooted with SU.
In my CM6, with a p3 1250 kernel, I am having an issue with Setcpu, SU and boot/reboot.
If I either boot or reboot in terminal, script or with the CM6 reboot screen, if I do not unlock my phone before my sd card has finished mounting, then setcpu does not get SU permission. The result is that in Setcpu, my slider shows 1250, but the running info bar above only shows 600/250. In the info screen, the cpu will actually clock to 700, but in neither case will it be actually running at 1250. If I touch the slider at 1250 then it changes.
The steps to try and duplicate would be to reboot/boot the phone, and do not use the slider or menu button to unlock, just let the phone sit for a number of seconds past when the sd card is mounted. When you finally open the screen, check setcpu to see if it is running properly. I did wipe and foactory reset a number of times when installing, I have cleared and reloaded setcpu, and cleared setcpu from SU to test.
If this is just my phone then perhaps I have an issue. If it is not just me, then it is possible to boot thinking you have a speed that is really not running properly.