I only know enough to be dangerous here, but I have a SoftLogix5800 engine running on my box. I'll assume you have the same.
If running XP on your box, go to Start/All Programs/Administrative Tools and select Services. From there, scroll down until you find the SoftLogix5800 Slot 1 service (your slot number may be different, depending on where your soft PLC resides in the virtual chassis). If the service is set to start up automatically, try changing Startup Type to Manual. I believe this will do what you want.