Hi
I think you need to enable PIT clock gate control, and FTM clock gate control, then you can see the correct register values.
SIM_SCGC6 |= SIM_SCGC6_PIT_MASK;
Please refer to the reference manual for more details about SIM_SCGC6.
Or you can run the demo Freescale\Freescale_MQX_4_2\mqx\examples\hwtimer to check the PIT register value
Regards
Daniel