Here's how to fix it:

In bin/JBuilder.config, the following lines are added:

  # JRun config
  include jrun.config

JRun.config contains the following lines:

  #
  # JRunWizard : JRun Integration for JBuilder  
  #
  # JRUNWIZARD_HOME - location where the wizard is installed
  # JRUN_HOME - location where JRun is installed
  #
  vmparam "-Djrunwizard.dir=D:\swdev\Borland\JBuilder7\projects\jrunwizard"
  vmparam "-Djrun.home=D:\swdev\Macromedia\JRun4.0"
  vmparam "-Dejipt.home=D:\swdev\Macromedia\JRun4.0"

  addjars D:\swdev\Macromedia\JRun4.0\lib
  addjars D:\swdev\Macromedia\JRun4.0\servers\lib
  addjars D:\swdev\Macromedia\JRun4.0\lib\ext
  addjars D:\swdev\Borland\JBuilder7\projects\jrunwizard\jbuilder-jrunwizard.jar

The problem is, the quotes around the terms after the vmparam tag. Change these to:

  vmparam -Djrunwizard.dir=D:\swdev\Borland\JBuilder7\projects\jrunwizard
  vmparam -Djrun.home=D:\swdev\Macromedia\JRun4.0
  vmparam -Dejipt.home=D:\swdev\Macromedia\JRun4.0

and the JBuilder will launch normally. Under the Tools menu, you'll see a JRun EJB Wizard menu item. Selecting it launches the JRun deployment wizard as expected.

It's not quite the seamless integration I'd like to see JBuilder 7 have with JRun 4, but it's a start.