I assume that you are also using the same PLL filter as they did between the XFC and VDD PLL pins? And a decoupling capacitor from VDD PLL to VSS PLL? Are your certain you are using the right values?
Is the oscillator circuit working properly? Have you measured the actual frequency? If there is anything wrong with it, the HCS12 will still work in "limp-home" mode around 2MHz, since the self-clock feature is enabled by default out of reset. All timing and baudrates will naturally be messed up, though.
