Hopefully I am not posting tons of messages, The site keeps giving me errors but I do not see my post.
Anyway... My Y axis is flipped compared to what is on-screen. Please see the below screenshots with what I am talking about and my settings. I would like to keep the settings so when I jog, the table moves left when I press left, up when I press up, etc.
The bottom PCB that you see is the correct one and the top is the two that I just milled. I did the correct one with EMC2 and it does work correctly so its just a matter of my mach3 settings somehow.