You should be able to play 3d blurays with PDVD13. It is not clear from you post if this is what you are trying and not succeeding.
The projector should be able to process a half side-by-side input to a s3d image (no special software needed, you play it as a 2d video); you may need to select SbS in the projector settings (it is not automatically recognized).
Netflixt 3d is not available on HTPCs, only selected LG (and Vizio?) tvs.
There are 3d threads in the more popular HTPC forum.