Luke,
What package size of the XEP256 are you using? If you are using a package size smaller than the 144 LQFP, you must also configure any unbonded I/O as outputs. By default, like the bonded out I/O pins, these are inputs after reset. See Section 1.2.3, Detailed Signal Descriptions, of the MC9S12XE-Family Reference Manual , Rev. 1.23.
Regards,
Gordon