Hi,
David is right. You must disable the SPI. Also you should set the Port Data Direction Register (DDRS for example) as output. I've tested this on DEMOAX9S12XEP100 board. See screenshots below (click on them to enlarge):
1. Initial state. SPI module initialized, but not enabled yet. The yellow marked address in memory window shows Port S Data Register (PTS) at 0x0248, Port S Input Register (PTIS) at 0x0249 and Port S Data Direction Register (DDRS) at 0x024A address.
As you can see Port S is set as input and PTIS reflects the buffered state on the pin which is 0xFC (taken from the PTS register). The MOSI pin (PS5) is logic 1.

2. SPI enabled. Port S dedicated to SPI module.

3. Port S set as output. SPI still enabled. the PTIS reflect the 4 SPI pin status: MOSI and MISO are high.

4. SPI disabled. Finally, PS5 (MOSI) pin is low as well as other Port S pins.

5. SPI enabled again. Doublecheck the Port S status. MOSI/MISO pins are high again.

Regards,
iggi