A and B will most likely need to be referred to a Fruit expert; are there any forums associated with the program? At a guess the difference will be that you used different compile-time options and that would explain the differences. The way to solve this would be to find out how the executable you downloaded was built - what exact commands were used, and of course which version of which compiler on which platform. This will all make a difference.
C in a sense, see A. It depends on what compile flags you use, and commercial compilers won't necessarily optimise better than free ones will. Don't assume that free=crap, find out why there is a slowdown first.