The problem was, when I dragged a folder into Fiji filled with a through-focus series of color .bmp files, it made 3 files for every 1 file, red, green and blue.  In this format, "Extended depth of field" could not process the images.  I found a fix.  It was to turn off SCIFIO.

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: C:\Users\JohnM\DOWNLO~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\JohnM\DOWNLO~1\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150813121940)
Fiji: http://fiji.sc/update/ (last check:20150814135156)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20140923152959 jars/jpedalSTD.jar
  9450678d (LOCAL_ONLY) 20150108140720 plugins/ExtendedDepthField.txt