IMHO, best practice to do something like this is writing a MBean. You can deploy your MBean with all its resources (.jar files, classes, property files, ...). Let your EJBs talk to this MBean proxy instead of doing the comm things directly.
Since I am not familiar with JAVA Comm, I don't know if it is using JNI. If so, be sure the needed .dll is in the jboss/bin directory or visible through your PATH.
I managed to set up a JMX Agent for my application and get it working outside of Jboss, and it looks straight forward enough now to get a servlet or ejb to access it, thanks for the tip.
The JAVA comm api for windows is definately the flakiest api I have worked with, it seems large directory filenames (greater than 8 chracters) or hierarchies (more than 2 directories deep) are enough to cause a failure.