3D Blu-ray uses MVC format. If you search for MVC you will find request for MVC support in SkyBox, and you can add your vote to those existing post threads.
In the meantime, your options are to not use SkyBox. Instead use Virtual Desktop + MPC-HD + MadVR etc. to allow decoding Blu-ray MVC directly to SBS for direct viewing without any lossy re-encoding (via Virtual Desktop).
Or, re-encode (lossy) all your Blu-ray rips into a SBS format, to allow viewing via SkyBox.
I believe we are all hopeful that MVC support will get some attention soon, especially with the new generation of cheaper and higher resolution headsets, making Virtual Home Theater finally a reality!
Just, in the meantime we need to re-encode all our Blu-ray's (or use Virtual Desktop etc, instead of SkyBox for our 3D Movie viewing).
