Okay. I found something that works well for me.
BluRay 3D Ripper version: 9.0.2.2
Profile: 3d.mkv.h264.audiocopy
SBS 100%
Video Decoder
H.264: CUDA
VC1: CUDA
MPEG2: CUDA
Video Decoder
H.264: Software + CUDA
Crop automatically is disabled in the conversion tab.
I have it on one-pass encoding with a custom bitrate of 20000. It will produce a huge file, but the quality is excellent without needing 2-pass.
I had those settings for Avatar 3D. The picture quality is excellent and the force subtitles worked to perfection. I only see the subtitles when they speak Navi. And there's no subtitle flickering.
Those force subtitles work in 3D viewing mode as well 2D viewing mode.