I'm not sure exactly what you're asking, but if I interpret it correctly in that you're wondering why intonation is the way it is, and why middle C and A(440) tend to be anchor notes scales are built from, I recommend the following book(s):

http://www.musimathics.com/

Very cool if you like math and music. The first volume covers what I just mentioned as well as the physics behind sounds and automated composition, and the second focuses more on audio DSP concepts.

At their current cost on Amazon ($45 a piece) they're a steal until some university somewhere makes it a required text ;)

Bryan