In the uploaded image, there are two light spots and two dark spots. If I do pixel integration on only the two light spots, I get
1) 10345.196
2) 11823.095.
If I then reset and integrate all 4 spots using the same selection box, I get
1) 3921.276
2) 4440.347
3) 15793.388
4) 16380.217

Why would the lighter spots integrate so much less when denser spots are included in the measurements?

Information about your version of Java:

  os.arch => amd64
  os.name => Windows Vista
  os.version => 6.0
  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-b18
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b18
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: PROTECTED_LOCATION

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~1\FIJI-I~1\Fiji.app/java/win64/jdk1.8.0_66//jre
  imagej.dir => C:\PROGRA~1\FIJI-I~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160121055533)
Fiji: http://update.fiji.sc/ (last check:20160114142236)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160121051645)

Files not up-to-date:
  13cf8fb2 (LOCAL_ONLY) 20160130185708 luts/glasbey_inverted.lut
  cad84490 (MODIFIED) 20160130185708 plugins/Examples/Fiji_Logo_3D.js
  a725934c (MODIFIED) 20160130185708 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py