When you have Jogged the motor using the Keyboard Jog header, did you also try Jogging it with the on screen arrows? If it is also inverted, you will have to invert the axis to move it in the direction you require: Planet-CNC/File/Settings/Axes/Reverse (check box) on the axis that is running in reverse.
The on-screen jog works properly, but the keyboard jog header runs the motors backwards. I had played with the software reverse function too, but couldn't get the on-screen and the keyboard pendant to work in the same direction. That's what lead me to check my wiring (maybe I had wires going to the wrong side of the header), and then to suspect a possible firmware error. I get the same story with all three axes.
I wanted to see if anyone else has any experience with the keyboard jog header.
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On B-Y-CNC USB Controller, I built a Kybd Jog pad to connect with on-board header. Jog seems to be backwards (Y+ moves it in the Y- direction). I've checked wiring. Could there be an error in the firmware?