To reproduce:
 - open a czi file containing multiple z slices, using Bio-formats importer with "Open as virtual stack"
 - Image > Transform > Rotate 90 Degrees Right
 - scroll through the stack
All z slices appear the same now, being copies of the slice that was active when performing the rotation.

On multi-channel images, the channels are retained (i.e. different images), but the z slices are lost (i.e. all copies of the same plane).

This bug seems to be specific for files opened via Bio-formats, since opening tif files via Import > TIFF Virtual Stack and then performing rotation works as expected.

Cheers,
Jan

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:\UTILIT~1\FIJI-L~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\UTILIT~1\FIJI-L~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150722045527)
Fiji: http://fiji.sc/update/ (last check:20150724215809)