Try hitting the Display button on your Onkyo remote next time you're playing a file. It's tell you the audio input and output specs the first time you presss it; the second time will give you the video specs e.g. 1920x1080p 60Hz.
Play a file that you know has DTS-HD MA sound, for example, or any other format that you know such as plain DTS, Dolby Digital (AC3). When you hit the display button, if you see the format name as it should be, you're bitstreaming. If you see LPCM, your software has decoded first.
I think it's likely that you're decoding if you're using Windows Media Player, and probably not even using the lossless tracks you ripped.
When you play the BD itself (the actual disc), which software is being used, e.g. Arcsoft TMT, Cyberlink PowerDVD, WinDVD etc.?