First, check to see that your project is actually using the derivative files mc9s12xdt512.h, mc9s12xdt512.c, and mc9s12xdt512.inc (for assembly). If the project is using other header files, you'll have problems.
Second, check to see if the compiler command line (use the HC12 Compiler Options settings panel) is set to generate code for the correct processor. It should be set to generate code for the HCS12X family (-CPUHCS12X). It shouldn't make that much of a difference, but you want to cover every possibility here.
---Tom