I misunderstood how you were using Lightburn… sorry. I did have a miniRambo board running Marlin at one time… though I had remapped the D9 fan pin to pin 10 (Z-min), and used M106/M107 for control, as I was using a Banggood/Eleksmaker laser that needed +5V PWM. I’m using Lightburn now but only to create the gcode… and don’t use “homing” so obviously can’t be much help beyond the suggestion I offered.
I spend a fair amount of time on the LB forum and often see others having “moves right manually but wrong-direction homing issues”… you might ask for help over there as well.