Hi @jetty_1012,
The Siul2_Port_Ip_Init() initializes the MSCR, IMCR and GPDO registers if the pins.
The "initial value" applies to pins in the GPIO mode.
The other drivers, such as the eMIOS, do not change the configuration, that means that even if the eMIOS is disabled, the pins are still routed to the eMIOS in the MSCR, IMCR registers.
If you want to be sure the pins are set as GPIO with some defined values, you can call the Siul2_Port_Ip_Init() again with a different structure.
The configuration tool can generate more structures.

Regards,
Daniel