Setting a Scara

I am trying to set a scara robot with a remora card, conected by ethernet, i can made to can work with the 4 motors that i need but when i try to put the scarakins. the joints work quite well,but when i home it i cannot move the axis on x and z. and i dont have any idea why this is happening.
 

  these is working right now but it works strange, in joint mode all the joint are great the j0=x(from the board), j1=y(from the board), j2=z(from the board) and j3=A(from the board) but when i home the robot, the motor j1 and the j3 change and i dont know how to change it, i think my hal is wired kind of well, but i dont know how to correct these, i tried to used a personalized kins but i get a lot of errors.