I don't know if I'm following this correctly but I think what you're saying: you set up your speakers with test tones to get them equal sounding all around. But when you play certain movies they seem to be unequal from front center to rear surrounds. If in these seemingly unequal channel movies do a test tone while in the movie. If the test tones still sound equal, then it doesn't seem to be mechanical. The movie is recorded in that fashion. What you're attempting is to remix the sound, in a sense, from the original mix.
That's my take. I could be wrong.