Why did you change the direction. I would start by putting those back and just physically flipping the plugs.
Your endstops should also have an option for either logic, I think they have a jumper, I haven’t used those in years though.
The dual has a ton of changes, for the most part it works as it should but I think you should start with just one change at a time and see what actually causes the issue, we are the only ones using it so beyond my standard settings I doubt any of the other logic has been confirmed. Your config-adv change does not ring a bell for me I don’t know what that does, it looks like you have reversed the Y axis twice?
What did you set the jumpers under your drivers to when installing them for the second X and Y steppers? Which drivers did you use? If they aren’t set to the same 1/32 or the new ones are 4988 instead of 8825 it would give those symptoms.
Yes! I'm using DRV8825s and two jumpers were missing due to an old usage of A4988 in the extruders, thank you!
Your endstops should also have an option for either logic
For this I used a simple A3144 wired directly to RAMPS, not the PCB endstop
it looks like you have reversed the Y axis twice?
I came up to this empirically, I believe one inverts if they go against each other which mine did (INVERT_X2_VS_X_DIR), the other inverts the + - of the axis (INVERT_Y_DIR)