When PLL is selected as the clock source on the MC9S12C64, when coming out of sleep mode, the PLL may no longer be selected in the CLKSEL register. The Processor Expert does not handle this correctly.
We had to add code to the macro in Cpu.h which waits for the PLL to lock before setting the bit in the CLKSEL register. That solved the problem. But this is something that should be taken care of by the Processor Expert generated code. Hopefully that can be corrected in a new release of CodeWarrior.