The only reasons I can think of why the Y motor direction would change are:
1. Firmware - as noted above, I made a change between 1.18 and 1.19, to bring RRF in line with other firmwares.
2. A change to the M569 commands in config.g, or an M569 command in some other file that is getting executed. [But AFAIK, no slicers generate M569.]
3. Reversing the Y motor connector, or swapping the wires of one of the phases in the Y motor connector. This could happen if you changed the Y motor cable.