I think some other people have been caught out with this but I seem to remember that most got round it with a direct connection to their LPT port, apparentl some isolating bob's have a particular pin that is a straight pass through as well.
Which setup have you used, I saw a nice one on the CNC zone forum, good description and links to the code needed, Im going to set one up soon, my bob is a simple pass through though so no problem with reversed polarities, my drives have the isolation built in.
Steve