I have been developing for 9S12DT256 for several years using CodeWarrior Pro and a P&E Micro USB-ML-12 BDM module version C. All of the drivers for the BDM are up to date as well as the firmware. I don't have the version of CodeWarrior available right now but I can provide it.
As soon as the PLL is enabled (first time I have ever used it) the debugger streams the error "The BDM has been re-enabled" several times and communication is lost.
My simple test program I am using to work this problem out just toggles a bit in a while loop. There is only a problem with the HiWave debugger. I tried the P&E debugger and it steps through the program fine and I have verified that the operating frequency has changed as it is supposed to, ie I can change the frequency of the output as desired by changing the PLL settings.