Orange LED? Yeah, I guess the "yellow" LEDs aren't really that pure a yellow. While LED is this that is briefly lit on power up.
Is the "Power On" LED on? This is the one near the header connector for the PMDX-407, and the silk screen says "Power On" (of course).
First thing to try is power off and remove ALL of the pluggable screw terminals except for the 2-pin power input (J19) and the 3-pin EStop connector. (J14) Also unplug the PMDX-407 from the 424. Power on the board, start Mach4 and see if the red LED turns off.
If not, try removing and re-installed the jumper wire or whatever that is in the EStop connector. If you have a meter, with J14 unplugged, measure the resistance between the center screw terminal and one one that would be closest to the corner of the PCB, if the connector were plugged in to the board.