If you include a substance file in your scene and customize its parameters, then save the file and re-open it on a different platform, your substance parameters may be lost when you re-enter the file path on the substance node.

To workaround this, open the .ma file in a text editor before opening it in Maya, and search/replace the substance file paths to fit the platform that you are going to work on.

For example, after you have saved a file in Windows and wish to re-open it on the Mac, search for C:\Program Files\Autodesk\Maya 2012\substances and replace it with /Applications/Autodesk/maya2012/substances. This way, on file load, your substance parameters should retain all animation and customization.