I fixed it! The problem was that even though I had it set as an INPUT in gpio.h as stated by Leonid, it is *not enough* to do this:
#define BSP_GPIO_INITIAL_STATE_PIN69 BSP_GPIO_INITIAL_STATE_INPUT_RECEIVER
Additionally, you must also change the Digi IOP MUX defaults from USE_2ND_PATH, to INTERNAL USE. I'm unsure of what consequences could come from changing these Digi defaults for the 9p9215. So far I have not found any. They may have been set this way for something that was part of the 9p9215's eval board? I think I am going to set all of mine to internal only in the event this could be causing some other issues.
//#define BSP_GPIO_MUX_IOP_0_GEN_IO_1 BSP_GPIO_MUX_USE_2ND_ALTERNATE_PATH
#define BSP_GPIO_MUX_IOP_0_GEN_IO_1 BSP_GPIO_MUX_INTERNAL_USE_ONLY
Alternatively you *can* reconfigure the pin in your own code. The reason it didn't work for me the first time, is that a neighboring pin which should have also been INPUT was also suffering from the same IOP MUX issue causing my pin 69 input to be pulled in the wrong direction.
Hope this helps someone else.