That’s strange. Any Z axis lockout should have nothing to do with the post processor. What Marlin firmware are you using? Is there a Z < 0 lockout enabled somewhere in configuration.h? I will take a look. Everything – Marlin, Fusion 360 and the post processor have been working fine for me and I have not looked at the firmware since last fall. I’m a bit rusty on it now.
As a test can you just give it some simple hand edited gcode to move the three axes below zero? http://reprap.org/wiki/G-code
I use a full graphics LCD/SD card and have not used Repetier in a long time. Is there a mode in Repetier to lock out axis like this?