Running a simple "import sys" in the Macro.ijm tool, with the language set to Python, will cause the Debug window to be flooded by "Waiting for 2 threads to die" messages as soon as the "script" is finished running. No other python code is necessary to trigger the bug, just the import statement. This renders the Debug tool almost useless, since any other debugging message will just flash by, and the only way to see it is to save the debug file and to find and read the relevant output in a text editor. While this bug is annoying, it may also indicate deeper problems with threading. The only way to stop the message flooding is to restart Fiji. 

A sample output of the debug window, including the first two "Waiting for 2 threads to die" messages, are included below:

--
setKeyUp: -1
actionPerformed: time=1399219884003, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=Macro,when=1399219884003,modifiers=] on menuitem0
runPlugIn: ij.plugin.NewPlugin("macro")
setKeyUp: -1
Not auto-importing ContrastPlot (is in both ij.plugin.frame and ini.trakem2.imaging)
Not auto-importing Channel (is in both ini.trakem2.display and script.imglib.color)
Not auto-importing Resizer (is in both ij.plugin and ij.plugin.filter)
Not auto-importing Selection (is in both ij.plugin and ini.trakem2.display)
Not auto-importing Overlay (is in both ij.gui and ini.trakem2.display)
Not auto-importing ColorPanel (is in both ij.gui and ij.plugin)
Not auto-importing GaussianBlur (is in both ini.trakem2.imaging.filters and ij.plugin.filter)
Not auto-importing FFT (is in both script.imglib.algorithm and ij.plugin)
Not auto-importing Normalize (is in both script.imglib.algorithm and ini.trakem2.imaging.filters)
Not auto-importing Process (is in both java.lang and script.imglib.algorithm)
Not auto-importing Compiler (is in both java.lang and ij.plugin)
Not auto-importing Histogram (is in both script.imglib.analysis and ij.plugin)
Not auto-importing Process (is in both ini.trakem2.parallel and script.imglib.algorithm)
err >Waiting for 2 threads to die
err >THREAD: Script Editor Run :: Sun May 04 18:11:38 CEST 2014
err >THREAD: org.python.google.common.base.internal.Finalizer
err >Waiting for 2 threads to die
err >THREAD: Script Editor Run :: Sun May 04 18:11:38 CEST 2014
err >THREAD: org.python.google.common.base.internal.Finalizer

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => D:\Fiji\Fiji.app

Information about the version of each plugin:

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