So, after some experimentation, EDID is the culprit. Output 1 on the splitter controls EDID communication with the source. Connecting the display to output 1 results in 3D video and stereo audio. Connecting the AVR to output 1 results in HD audio and no 3D capability. I knew this was too good to be true but I hoped against hope it would work. I'm giving up on the idea of 3D and HD audio without spending on a new AVR.
3/14/14 at 9:32pm