Two issues -
1. dialog boxes that are blank except for the "ok" or other buttons
Even when starting FIJI, I get a blank dialog box because I have a duplicate plugin. If I click outside of FIJI, the text in the box often appears. It becomes confusing when I have many windows open and don't know what FIJI is trying to communicate to me. This makes FIJI difficult to use (although I keep trying) and I switch to ImageJ which normally works and I can read the dialog boxes.

Interestingly even when trying to submit this bug report I got a blank dialog box which I later found out told me the submission failed.

2. Sync Windows often gets a step behind.
When I have synced windows, often if drawing a rectangle in one window, it will draw in the others but not the target window. Sometimes clicking outside of FIJI corrects this. Often, particularly if my computer sleeps, the synced windows command is very problematic. If it allows me to select a line or rectangle, it seems to cause blank histograms, and blank profiles. It applies the magnifying glass tool nonuniformly across the windows, apparently does not allow use of selecting tools (rectangles, ellipses, lines...). Sync Windows is problematic in FIJI and ImageJ.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.1
  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-b14-468-11M4833
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-468
  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:20151026125651)
Fiji: http://update.fiji.sc/ (last check:20151028083859)

Files not up-to-date:
  2076fd3d (LOCAL_ONLY) 20090804144631 plugins/Analyze/Auto_Corr.class
  f1391319 (LOCAL_ONLY) 20040717102226 plugins/Analyze/Calculator_Plus.class
  36fcde8c (LOCAL_ONLY) 20090803142749 plugins/Analyze/Covariogram_.class
  d68c83b7 (LOCAL_ONLY) 20020502064914 plugins/Analyze/Radial_Profile.class
  2c75ef55 (LOCAL_ONLY) 20110316153527 plugins/Analyze/Radon_Transform.jar
  4deea97d (LOCAL_ONLY) 20140506194310 plugins/KHKs_Utilities.jar
  a095c0ae (LOCAL_ONLY) 20140730085721 plugins/Substack_Maker.class