Can you post a picture of the configuration screen on the Onkyo? Have you run AccuEQ or manually calibrated speaker distance and level? The effect may be very subtle in some movies. I haven't tried TMNT yet, but Transformers 4 was a disappointment to me. Try the Dolby surround upmixer with a standard movie soundtrack or even some two-channel audio and your height speakers should be active. There is a demo disc from Dolby but it was distributed to retailers and other contacts within the industry. Good luck finding one.
Yes I ran EQ. There were parts of TMNT that I could here the overhead channels pretty good, you need to try that movie.