I have 2 image stacks with identical fields of view and positions but with different resolutions.  The pixel size properties are set accordingly.  However, when an ROI is created on one image set and transferred to the other image set, it is placed in a wrong position, as if the pixel coordinates were used instead of the real physical coordinates.  

This happens when the transfer is done via restoring the ROI or via the ROI manager, or via an *.roi file.  Moreover, because the roi file appears to be binary and quite complicated, there is no easy way to work around this problem.  I have to resample one of the stacks, obviously not a great solution.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 4.1.15-gentoo-r1
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b17
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b17
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: READ_ONLY

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/local/Fiji.app/java/linux-amd64/jdk1.8.0_66//jre
  imagej.dir => /usr/local/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217100804)
Fiji: http://update.fiji.sc/ (last check:20160218085537)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160318092131)