I am working on a project where I make a HAT for the Jetson Nano dev kit. (essentially a pi4 with GPU) I am powering the JN with my HAT, which provides 5V to pin 2&4 of the JN. I have a few buttons connected to the JN which are pulled up with a 10k resistor. (see picture) I have verified the workings of the switches without the JN attached, they are 3v3 when inactive, when switch is pressed they become 0v. I have also verified the working of the GPIO pins by connecting GND and 5V to it, and it read it correctly. I also tested if the pin is floating if not connected, and that seems to be the case as well.
This is where the strange behavior starts: when I connect the HAT to the JN, and set pin 7/BCM4/GPIO126/SW_Off to INPUT, the inactive-voltage drops from 3v3 to 0.98V. This way the GPIO is useless, could anyone explain how this could happen? What other steps can I take to tackle this and find out how to resolve this? If it is useful at all, I included the board layout. I verified that R4 measured 3v3 on 'topside' (relative to both HAT and JN, their grounds differ 6mV), however I measured 0.98V on the other side. Any help greatly appreciated!
Edit: it might be good to mention that the top connector in the layout is the 40 pin connector, the middle stop is the resistor, and the bottom smd pad is the switch connector.
Edit: The resistance measured to ground (with power off) is 11.78K, and the resistance measured to +3.3V is 10K. This calculates to a voltage of 1.78 Volt, but measures as 1 V when the system is on. Any suggestions as where the resistance to ground could be coming from?