Running the following macro:

run("Fluorescent Cells (400K)");
run("Flatten");

will throw the exception pasted below. The exception is thrown only if the current image is in *Composite* mode, and independent of an overlay or ROI being displayed.

********************
(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49f; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.4; 26MB of 4491MB (<1%)
 
java.lang.IllegalArgumentException: DirectColorModel required
	at ij.process.ColorProcessor.setColorModel(ColorProcessor.java:101)
	at ij.process.ImageProcessor.setLut(ImageProcessor.java:184)
	at ij.CompositeImage.setup(CompositeImage.java:131)
	at ij.CompositeImage.reset(CompositeImage.java:527)
	at ij.ImagePlus.setStack(ImagePlus.java:672)
	at ij.ImagePlus.setImage(ImagePlus.java:521)
	at ij.plugin.RGBStackConverter.compositeImageToRGB(RGBStackConverter.java:176)
	at ij.plugin.RGBStackConverter.compositeToRGB(RGBStackConverter.java:76)
	at ij.plugin.RGBStackConverter.run(RGBStackConverter.java:38)
	at ij.plugin.RGBStackConverter.convertToRGB(RGBStackConverter.java:63)
	at ij.process.StackConverter.convertToRGB(StackConverter.java:171)
	at ij.process.ImageConverter.convertToRGB(ImageConverter.java:85)
	at ij.ImagePlus.flattenStack(ImagePlus.java:2420)
	at ij.plugin.OverlayCommands.flattenStack(OverlayCommands.java:276)
	at ij.plugin.OverlayCommands.flatten(OverlayCommands.java:261)
	at ij.plugin.OverlayCommands.run(OverlayCommands.java:34)
	at ij.IJ.runPlugIn(IJ.java:172)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:61)
	at java.lang.Thread.run(Thread.java:695)
********************

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  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: null
  imagej.dir => /Users/eglinger/Fiji-debug/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140822175924)
Fiji: http://fiji.sc/update/ (last check:20140821133247)