When I try to run the following code in Javascript:

importClass(Packages.ij.IJ);
importClass(Packages.ij.plugin.frame.RoiManager);
importClass(Packages.ij.io.OpenDialog);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.java.io.File);
importClass(Packages.ij.gui.GenericDialog);
importClass(Packages.ij.util.Tools);
importClass(Packages.ij.plugin.Duplicator);
importClass(Packages.ij.measure.ResultsTable);
importClass(Packages.ij.ImagePlus);
importClass(Packages.ij.process.ImageProcessor);

IJ = IJ();
rm = RoiManager.getInstance();
rt = ResultsTable.getResultsTable();
if (rm==null) rm = new RoiManager();
if (rt==null) rt = new ResultsTable();
//var procName = "MC21_w1cf-Brightfield_s1-0001proc.tif";
//IJ.selectWindow(procName);
impProc = IJ.getImage();
rm.select(impProc, 0);
ipProc = impProc.getProcessor();
stats = ipProc.getStatistics();
mean = stats.mean;
print("The mean is: " + mean);

stats2 = impProc.getStatistics();
mean2 = stats.mean;
print("Mean2 is: " + mean2);

I get the following output:

The mean is: 14891.73076923077
Mean2 is: 14891.73076923077

However, if I go to the graphical user interface and do analyze, measure, I get a different answer:

18444.4111

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  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 => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150501134914)
Fiji: http://fiji.sc/update/ (last check:20150520024906)

Files not up-to-date:
  b916ac8e (MODIFIED) 20150801204012 jars/ij-1.49s.jar
  ed67c174 (LOCAL_ONLY) 20150522025708 plugins/Versatile_Wand.class