I may be asking the obvious but have you done the following (as described in the manual):
Jumper J27 must be disconnected before programming. After programming,
reconnect J27 to enable the reset line for the SBC.
The S12 family is using a programming interface called BDM (background debug mode). The BDM programming pod pulls the reset pin low before trying to access the CPU.
Roger that Lundin, I have seen some systems that have a power supply watchdog or other interface to the reset line that (whatever) BDM programmer interface the developer is using doesn't have enough pull to override the current state. In any case, our poster has probably had his answer solved already.