Well if it's for stopping inadvertently running the 3rd party application and you aren't trying to definitively block it happening.
Write a little application that launches this here Microstation and does WaitforSingleObject. Before it launches it checks against some central resource, if Okay, ups the count of that resource. When microstation closes it decrements.
Replace all the shortcuts for Microstation with the launcher app and you have something that will do the job for minimal effort.
You could even beef it and respond with who/where all the five instances are, and deal with per-machine / per-user if it's relevant.