What does the machine show if:
- You move to the MIDDLE of the table and zero everything, and move the TOOL to the left? Number on the DRO positive or negative? Does the LEFT arrow produce LEFT tool movement?
- Now back at 0,0.... Does the up arrow move the tool towards the back of the table? What does the DRO show, positive or negative?
Inverting the signals may not be what you need but I used inverting only to get the axis moving in the direction that agreed with the arrow keys for left/right and front/back. That is independent of where the switches are located. You config tells the machine what coordinate is applied when you home against the switch. I'd suggest seeing if you can get it to behave as expected without the switches configured.
Get it moving correctly and make sure that when you manually move the tool to the left front of the table and set that as home that it zeros the machine coordinates (switch the DRO to machine not relative) and that from there, moving to the back right produces positive X and Y values. Until that is right your going to go insane trying to fight with the homing procedure.