So in short, when running a macro in headless mode from the command line, the sigma parameter of the standard Gaussian Filter seems not to be captured by the macro interpreter. 

Here is a dummy example: 

open('path-to-image'); 
name = getTitle() 

run("Duplicate...", "title=Dup"); 
                                                    
run("Gaussian Blur...", "sigma=5"); 
save('gaussian1.tif'); 

selectImage(name) 

run("Gaussian Blur...", "sigma=1"); 
save('gaussian2.tif'); 

When calling this macro from the Fiji in Gui (so normal) mode, everything works as expected. 
But when calling this macro from the commandline like 'ImageJ-macosx --headless -macro dummy.ijm' 
the two produced images will be the same, meaning that sigma most likely was set to a default value. 

See also my post and the replies on
 http://imagej.1557.x6.nabble.com/Gaussian-Blur-Filter-in-headless-mode-broken-td5011489.html#a5011505

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.1
  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-b14-466.1-11M4716
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  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: READ_ONLY

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Volumes/Fiji/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150122044514)
Fiji: http://fiji.sc/update/ (last check:20150127132630)