As the Dir signal changes as expected, it can't be a endstop/firmware problem. Also, if M119 reports what's expected, endstops actually do work fine.
Did you solder the pins into the Pololu? I had cases where people considered these holes in the PCB to be a pluggable connector.
Did you solder the pins into the Pololu? I had cases where people considered these holes in the PCB to be a pluggable connector.