Hi G.w. Sun,
Please see the image below for a simplified example. In this example, I have FSOB, PGOOD, and INTB pulled high by the recommended resistor values. I then have them being sensed by the GPIO pins of an i.MX 8M Mini. However, when configured as an input, the leakage current into these pins is about 15uA. Because of the high resistance, the leakage current is causing there to be a 1.5V drop across the pull-up resistor (15uA * 100k ohms = 1.5V), making it appear as though the lines are low when they aren't.

Does that help explain what I mean when I said that my input pins have large leakage currents?
Thanks