Enable classpath file mode popup doesn't work

I'm trying to generate Javadoc for our project, and the red error popup displays:

Error running Javadoc:
Command line is too long. In order to reduce its length classpath file can be used.
Would you like to enable classpath file mode for all run configurations of your project?
Enable

Clicking the "Enable" link doesn't seem to do anything.  The popup stays there until I access another part of the IDE.  Then when trying to generate Javadoc again, the error popup redisplays.

Is there a way to enable classpath file mode for all run configurations other than the error popup?