Open any image with SCIFIO enabled (Edit > Options > ImageJ2)
or create your own image with 

  newImage("BugTest", "8-bit black", 100, 10, 1);
  saveAs("Tiff", "/Users/eglinger/Desktop/BugTest.tif");

and then open it.
Then, 'Image > Transform > Rotate 90 Degrees Right' or the macro code

run("Rotate 90 Degrees Right");

will result in the following exception:

(Fiji Is Just) ImageJ 2.0.0-rc-6/1.49b; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.3; 220MB of 3011MB (7%)
 
java.lang.ClassCastException: ij.gui.ImageWindow cannot be cast to ij.gui.StackWindow
	at ij.ImagePlus.setStack(ImagePlus.java:634)
	at ij.plugin.filter.Transformer.run(Transformer.java:61)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
	at ij.IJ.runPlugIn(IJ.java:173)
	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 => 10.9.3
  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:20140623222553)
Fiji: http://fiji.sc/update/ (last check:20140624002555)