In order to route 3D content easily via a matrix switch or splitter, ALL connected displays need to be 3D compatible. Even, if just one of the displays is not 3D compatible, the 3D source player will NOT output the 3D content. The HDMI handshaking process will trigger the source player to drop it’s resolution output so that all displays can show content.
The problem is HDMI is designed such that the source ‘polls’ the EDID data (EDID is a display’s identity card stating what it’s capabilities are, a bit like a top trumps card) from all connected Sink devices (your 3D enabled display and non-3D enabled AVR) and outputs the lowest quality video signal all devices support (2D in your case).
To ensure 3D IS routed via the Matrix Switch or Splitter, the non-3D compatible display device must not be ‘active’. Sometimes turning the display into standby will be sufficient and sometimes full power off is required.
Essentially, the 3D source player must not be able to ‘see’ a 2D only display connected to the Matrix Switch or Splitter.
For best results when using 3D Blu-ray – HD Connectivity recommends… not actually connecting your 3D Blu-ray (BR) player to the Matrix. As Blu-ray 3D content is generally only viewed at a single ‘main’ TV location, in this instance it is better to have a direct connection between source and display, bypassing the Matrix completely. This will avoid any potential for ‘black screen’ situations at the other TV locations. It will also ensure that absolutely the best 3D format is selected for use on that display, not a potentially reduced quality 3D format that a lower 3D-capable display, connected to the matrix can influence the 3D BR to output. (Plus wearing those massive 3D glasses all around your house is really not cool and could result in you bumping into doorframes! – Ed)