Hello,
No, the 1.2 voltage is higher than it should be if there is nothing programmed. I have tested this with our freedom board by doing a mass erase. The voltage on those pins ranges between 0 and 5mV.
I recommend that you do a mass erase and try to test the pins again.
As for intializing the GPIO, I recommend downloading the SDK from our website, which has multiple examples that can show you how to to the proper setup for these pins.
In addition, you can check chapter 63 of the reference manual for further information.
Best Regards,
Sabina