several people have emailed amcas and asked about this. many of the responses are posted if you search. the bottom line is that they tell you to base your decision on how to clasify by the subject material, not the course designation or the department that taught the class.
for me, i had maybe 1/2 to 1/3 of my engineering classes counted as math or physics, with 1 or 2 chemistry. just think: would a physics/math/chemistry major take a class in this (undergrad or graduate level)? compressible flow - yes, finite element modeling - no, aerothermochemistry of propulsions systems - yes, aircraft stability & control - no, astrodynamics - yes.... and so on. just be able to defend your decisions to yourself. none of my designations were changed by amcas.
ps. sorry for any typos.. having a couple cold ones watching georgia/florida game..... reading up for some interviews this week...