The default frequency for the PSoC is 3MHz. So, as soon as the program is downloaded to the debugging pod, the CPU speed is shown as 3MHz in the debug window. When the PSoC is loading the configuration in boot.asm it is actually running at 12MHz no matter what the CPU clock setting. So, when a break point is set in boot.ask, the CPU speed will be shown as 12MHz in the debug window. The CPU clock is updated to the value set in the global resources just before the call to main. So, if a break point is set at the beginning of main, the CPU clock will show the actual value set in the global resources.