That message is because you are outwith the SoftLimits you have set up. Disable the softlimits so you can jog but obviously be careful as you jog as there will not be any soft limit protection.
If you swapped the drives and the problem stayed with the axis then carefully check the wiring to make sure it is OK, if it is then if you have a volt meter disconnect the port cable from the breakout board and check between your Dir pin and a Gnd pin on the cable. The Dir pin voltage should change between 0v and 5v depending on direction you jog. If it does then it is likely your breakout board.
Hood