Labeled image of the connections here:
Usually problems with homing are mis-plugged / swapped switches — yours doesn’t sound like that, since it gets past the homing operation — the not backing off the switches is odd — if the defaults actually are being retained, then I suspect that there’s some deeper problem. If the standard troubleshooting things (power down, reset PRAM and SMC if using a Mac, uninstall and reinstall the driver and attendant apps) then contact support@carbide3d.com and we’ll help you determine the difficulty.