Thanks for pointing that out, unfortunately setting display width/height and setting stereoscopy to 11 didn't change anything. I am now watching my 3D SBS videos as 2D then using my TV to do the conversion. It works but the picture quality isn't as sharp, and I can't work out why. I've found a few other issues:
1. A separate problem, since upgrading to 1.0.9, sometimes in the middle of a video stops playing and turns into this:

2. And the final problem, not specific to 1.0.9, I could also reproduce this problem in 1.0.8 and 2.0.0:
When I set audio to RAW 5.1, all my lossless codecs (DTS-HD, TrueHD) becomes the lossy variants (DTS, Dolby Digital Surround). While my AAC 5.1 plays as 2.0 (in 2.0 and 1.0.9) and 5.1 (in 1.0.8 )
When I set audio to RAW 7.1 or Auto, all my lossless codecs play fine, but AAC 5.1 outputs as PCM zero (no audio).
Is this by design, or a bug?