Check out this thread:
http://forum.arcadecontrols.com/index.php/topic,72750.40.htmlOn page two, there is a discussion about the problem you are having.
I used a pnp transistor to disable opto isolators that I used to isolate the drive from the printer port.
looking back, this was probably over kill.
Reference my post on page two dated November 15,2007 to see a diagram I posted.
You could just as easily use this transistor to disable your drive by attaching the transistor between the drive's enable pin and +5vdc.
If the LPT output is high, no current flows to the drive enable.
But if the output is low, the transistor turns on and puts +5vdc to the drives enable pin, allowing it to run.
The very first thing Mrotate does is set all the printer port outputs to low. So this worked pretty good for me.