When I close Fiji, the process continues to run in the background.

Here is the command-line output when I start Fiji:

$ /usr/share/Fiji.app/ImageJ-linux64 --java-home '/usr/lib/jvm/jav7-openjdk-amd64'
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[ERROR] Skipping unsupported option -port7

Here is the output when I close the window:

Exception during disposal:
java.lang.reflect.InvocationTargetException
	at java.awt.EventQueue.invokeAndWait(EventQueue.java:1272)
	at java.awt.Window.doDispose(Window.java:1209)
	at java.awt.Window.dispose(Window.java:1147)
	at ij.ImageJ.run(ImageJ.java:767)
	at net.imagej.legacy.IJ1Helper.dispose(IJ1Helper.java:246)
	at net.imagej.legacy.ui.LegacyUI.dispose(LegacyUI.java:127)
	at org.scijava.ui.DefaultUIService.dispose(DefaultUIService.java:362)
	at org.scijava.Context.dispose(Context.java:376)
	at net.imagej.legacy.DefaultLegacyHooks.quit(DefaultLegacyHooks.java:100)
	at ij.ImageJ.quit(ImageJ.java)
	at ij.plugin.Commands.run(Commands.java:45)
	at ij.IJ.runPlugIn(IJ.java:171)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.IllegalArgumentException: null source
	at java.util.EventObject.<init>(EventObject.java:56)
	at java.awt.AWTEvent.<init>(AWTEvent.java:337)
	at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:224)
	at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:188)
	at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:150)
	at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907)
	at java.awt.MenuComponent.removeNotify(MenuComponent.java:310)
	at java.awt.Menu.removeNotify(Menu.java:198)
	at java.awt.Component.removeNotify(Component.java:6980)
	at java.awt.Container.removeNotify(Container.java:2800)
	at java.awt.Window.removeNotify(Window.java:782)
	at java.awt.Frame.removeNotify(Frame.java:1041)
	at java.awt.Window$1DisposeAction.run(Window.java:1190)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:241)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
	at java.awt.EventQueue.access$200(EventQueue.java:103)
	at java.awt.EventQueue$3.run(EventQueue.java:694)
	at java.awt.EventQueue$3.run(EventQueue.java:692)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.awt.EventQueue$4.run(EventQueue.java:708)
	at java.awt.EventQueue$4.run(EventQueue.java:706)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Thanks!
Adam

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.11.0-24-generic
  java.version => 1.7.0_55
  java.vendor => Oracle Corporation
  java.runtime.name => OpenJDK Runtime Environment
  java.runtime.version => 1.7.0_55-b14
  java.vm.name => OpenJDK 64-Bit Server VM
  java.vm.version => 24.51-b03
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/lib/jvm/java-7-openjdk-amd64/jre
  imagej.dir => /usr/share/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140623162553)
Fiji: http://fiji.sc/update/ (last check:20140623182555)

Files not up-to-date:
  0d538731 (LOCAL_ONLY) 20140604135013 plugins/PhiDM_Version4_1.class
  e768f18b (LOCAL_ONLY) 20140623155730 plugins/jars/commons-math3-3.3.jar
  bd1f4461 (LOCAL_ONLY) 20140623155740 plugins/jars/jtransforms-2.4.jar