Maybe this can help you out:all my printers are with duet2 wifi, and upon building a printer for a friend with the hardware that he already had included a skr 1.3 and tmc2208 deivers, i came across reprap firmware for lpc boards and so i installed that port of reprap firmware to skr 1.3, and all and all was perfect.. my friend also has a btt tft32 that wanted to have it instaled(after i told him that with reprap firmware you dont need an lcd he still decided to have lcd)
So i installed the lcd to the skr1.3 board and in the config.g file i specified raw mode and i was suprise to see it working...i can do all things from lcd as it was under marlin firmware...nevertheless i have as well an mks 32tft lcd and tryed that lcd and again all working just fine...
That was definitely it. I swapped the wire around it works fine. What is interesting, is I have two duets. My other duet has a simple endstop inserted to E0 endstop. Also the wire is inserted at 180 degree rotation as compared to the board giving me issues. weird.
One last thing-- I tried the stock config home all and home z files, and they did not properly work. Yours did work for me. Thanks, as I still needed those changes.