Hi Neil
Did you remember to configure the Port TA pin assignment register for its primary (GPT) functions rather than GPIO? Without this, the signal will not be routed from the external pin to the GPT module.
The code you need is:
MCF_GPIO_PTAPAR = MCF_GPIO_PTAPAR_PTAPAR3(0x1) |
MCF_GPIO_PTAPAR_PTAPAR2(0x1) |
MCF_GPIO_PTAPAR_PTAPAR1(0x1) |
MCF_GPIO_PTAPAR_PTAPAR0(0x1);
CFInit includes a dialog for configuring pin assignments.
Hope this helps
Simon