If you're watching movies with AAC soundtracks, those particular movie files are almost certainly only 2-channel stereo just in terms of the audio that is actually present in that movie file.
If you want to listen to 2-channel stereo recordings using all 5 or 7 speakers and your subwoofer, you need to use the Dolby Pro Logic IIx listening mode. So press the "receiver" button on your Onkyo remote to make sure it is controlling the receiver, then press the "TV/Movie" button (it should be the leftmost button in that row) until you get DPL IIx as the listening mode.