I figured out the difference.
My 2003 server has been in production for a long time. Some attributes like "WhenChanged" do not replicate. The "WhenChanged" attribute updates each time a change is made.
My 2008 server is new. Some of these types of attributes that change "incrementally" have smaller values than the older 2003 server which may have an object that has changed many, many times.
The difference between my exports was about 2Kb a user, but over 20,000 users, the exports started looking vastly different in file size.
Way too much nerd-dom for one week