I think this issue started when I upgraded to El Capitan, but it may have been when I updated to Java 8. In either case, there are a lot of little issues. I've seen a few of them in the forum.

1) Clicking the FIJI icon in the dock opens up a new java instance. I can't drag and drop files onto the instance.
2) metadata is no longer parsed correctly from our DV files (DeltaVision)
3) Often, when clicking from window to window I lose the all of the menu bar disappears except for the ImageJ menu. It can take a while for it to come back. 
4) performance is very slow and seems to deteriorate over time. Sometimes it will take 30s just to responde to changes using the brightness/contrast tool. (opening the bug report form took ~1 min)

Thanks for your help!

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.1
  java.version => 1.8.0_65
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_65-b17
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.65-b01
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  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: UPDATEABLE

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:20151026145651)
Fiji: http://update.fiji.sc/ (last check:20151026052036)