Try this. Add this line to the end of the eclipse.ini file (not sure if the file is named the same in JBDS, but there should be an ini file in the base directory):
-verbose:class
Then run the console version of Eclipse (eclipsec.exe). This version opens a console window. Make sure you have set up Command Prompt screen buffer height to a large number, you're going to get a lot of output and you don't want it scrolling out of the buffer. Actually, you might want to start eclipsec.exe from the ocmmand line and redirect stdout and stderr to a file:
eclipsec > output.log 2>&1
Run your build/tests until you get the error. Exit Eclipse and open up that file.
This option causes the JVM to print the name of every class that was loaded and the full path for the JAR file that contains the class. This should help you find where the "hidden" JAR file is located.