Hi Spaded21,
regarding your encodes resulting in 2D, check your __ENCODE_3D_MOVIE.avs file if the views are inverted:
Code:
# Current base view: right eye!
# The views are inverted: AVC stream = right view, MVC stream = left view.
right = SelectEven(interleaved)
left = SelectOdd(interleaved)
if that's the case it's probably the bug with FRIMSource MVC decoder to blame. I suggest downloading the latest version of BD3D2MK3D as it's got a newer version of this 3rd party library and have another go.
You can also read more about the bug quite recently reported
here and
here