Let me say that I have no idea what you "template" is, so the following may not be applicable to you.
Without seeing the files, it's impossible to say what's going on. In Adobe Acrobat Pro, select File>Save As>Optimized PDF, then click on the "Audit space usage" button on the optimize dialog. This will tell you what type of elements are using how much space in your PDF file. When you compare the there sets of numbers (each document separately, and then combined), where do you see the difference? What if you combine both files in Acrobat and not in Word?
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com