FWIW, I just watched the same movie* on both Netflix and Amazom Prime. both were dolby Digital 5.1 and where Netflix made the nasty noises, Amazon Prime did not. Conclusion: Not my equipment or setup.
Boo on Netflix.
* Hansel & Gretel: Witch Hunters. Don't laugh. It's fun, doesn't take itself amy more seriously than it has to and makes pretty good use of the surround channels, particularly in the beginning.