Hi I also had the same trouble as you with the y axis and it wouldnt home properly, eventual found that the endstop was wired wrong with the 2 wires close together on the plug instead of 1 either end as in the pictures in the manual. Also mine had the auto level option and this to was wired wrong but on the mainboard end causeing the lcd display to not work properly. uploading the hex file didnt seem to do anything with autolevel either so source code or at least the config file would be helpful.hope this helps.
Geoff
Geoff