The term 'science GPA' is really a misnomer. What everbody calls the science GPA when discussing the AMCAS application is really the BCPM GPA which is only for Biology, Chemistry, Physics, and Mathematics courses.
I believe that AMCAS did it this way because there are too many pseudoscience courses or courses in which your performance may not be a good indicator for performance in medical school (things like Geology or Forestry).
It sucks for some people that major in say Geology, since if they do well, they can't include many of their courses. But if you major in Physics, just about all your courses will be included in the 'science' GPA since you take mostly Mathematics and Physics courses. Of course, if you do poorly in these...ouch!
Hope this clears things up for you.