It is always easier to check when we have a project to play with. Can you please post your complete project or a shortened version that shows the issue so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
Your problem might be that the SCB pins are dedicated and may not be changed freely.
Most of the hardware connections for the SCB are direct connections to specific pins. Since these connections are dedicated, I2C, SPI and UART can be connected to dedicated pins only.