port configuration help req.

I have been using an old 386 for a project and last week I picked up
another that had been left out for the garbage. I connected the
computer up and it booted ok and I installed my software (maxpro). I
connected up my controller and strange things started to happen! The
x axis works ok but I have no y axis yet when I jog the z axis both
the z and y move. Changing back to the previous computer all was well
again.
Any ideas please?
Thanks, T. Ackland