ok, have you tried disabling dram ecc?
the file you have attached has no change from the setting nvidia is doing for these pins.
But you have your custom board. What devices are connected to these pins and what is it used for? Interrupt purpose?
one possibility could be
in devkit, cboot tries to communicate with the gpio expanders whose interrupt lines are GPIO_EXP1_INT and GPIO_EXP0_INT. Since your board has a different device connected, it can be possible that due to some activity, interrupts are getting generated?
You can try commenting the below code in cboot code and rebuild cboot.
err = tegrabl_tca9539_init();
thanks
Bibek