@pup_hime hmm, couple things we can think of
when many cheeses melt, they separate and lose a lot of oils, and that separation and/or lack of oil might affect the flavor
When cheese that has been stabilized (usually using sodium acetate) melts, it doesn't separate--but that cheese has sodium acetate in it, which is salty, so that affects the taste
When cheese melts and oozes out onto the pan, or melts at high temperatures in an oven, it browns (if it doesn't burn) and that changes flavors
-F