When a scale bar is inserted into an image that is then used as the last image in a stack and converted to a montage using Image>Stacks>Make Montage... the scale bar is lost from the resulting montage. However, when the image with a scale bar is first saved as png (it does not work when the image is saved as tif), then closed and reopened before making the montage, the scale bar is maintained in the montage.

Minimal macro that reproduces the issue:
newImage("1", "8-bit black", 1392, 1040, 1);
newImage("2", "8-bit black", 1392, 1040, 1);
run("Scale Bar...", "width=100 height=10 font=60 color=White background=None location=[Lower Right] bold overlay");
run("Images to Stack", "name=Stack title=[]");
run("Make Montage...", "columns=2 rows=1 scale=0.25 border=4");

Minimal macro with a workaround for the issue:
dir=getDirectory("Choose Source Directory");
newImage("1", "8-bit black", 1392, 1040, 1);
newImage("2", "8-bit black", 1392, 1040, 1);
run("Scale Bar...", "width=100 height=10 font=60 color=White background=None location=[Lower Right] bold overlay");
saveAs("png", dir+"2.png");
close();
open(dir+"2.png");
run("Images to Stack", "name=Stack title=[]");
run("Make Montage...", "columns=2 rows=1 scale=0.25 border=4");

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Programs\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\Programs\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217160804)
Fiji: http://update.fiji.sc/ (last check:20160218145537)