What is the GPIO's default state after power up or hardware reset?
It should be tri-stated
From my tests, IO is HighZ state under Reset.
If ConfigIOMatrix is run, some IO will go to Output state. E.G. you set UseSPI=False, some SPI pins still goes to Output, NOT HighZ as you may wish / think.
So set other side IO to HighZ and Release it until FX3 send out a signal.
I have also faced this issue, FX3 is driving all the GPIF lines after power up to Low. Please let me know is there any setting we need to make to make these pins as high impedance.