Thanks for the pointer, I wasn't using Init_GPIO just fsl_gpio and pin_mux. I've added Init_GPIO and enabled the clock gate as you've shown however it hasn't made a difference. Anything else that could have an effect?
The pin_mux.c file seems to be generated correctly as it has the following.
/* Affects PORTC_PCR12 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,12UL,false);
PORT_HAL_SetMuxMode(PORTC,12UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,12UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,12UL,true);
/* Affects PORTC_PCR13 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,13UL,false);
PORT_HAL_SetMuxMode(PORTC,13UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,13UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,13UL,true);
/* Affects PORTC_PCR14 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,14UL,false);
PORT_HAL_SetMuxMode(PORTC,14UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,14UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,14UL,true);
/* Affects PORTC_PCR15 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,15UL,false);
PORT_HAL_SetMuxMode(PORTC,15UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,15UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,15UL,true);
/* Affects PORTC_PCR16 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,16UL,false);
PORT_HAL_SetMuxMode(PORTC,16UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,16UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,16UL,true);
/* Affects PORTC_PCR17 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,17UL,false);
PORT_HAL_SetMuxMode(PORTC,17UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,17UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,17UL,true);
/* Affects PORTC_PCR18 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,18UL,false);
PORT_HAL_SetMuxMode(PORTC,18UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,18UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,18UL,true);
/* Affects PORTC_PCR19 register */
PORT_HAL_SetPassiveFilterCmd(PORTC,19UL,false);
PORT_HAL_SetMuxMode(PORTC,19UL,kPortMuxAsGpio);
PORT_HAL_SetPullMode(PORTC,19UL,kPortPullUp);
PORT_HAL_SetPullCmd(PORTC,19UL,true);