Given we're still in the early days it could be something about the specific files I'm using to test, buuuut:
Trying a video file with side-by-side 3D, it seems like it works as expected. Top-over-bottom, something strange. When the controls/progress bar are showing, the video looks good. However, when that's sent away it seems like the video loses vertical alignment. The majority of the picture in the middle my eyes can still handle, the depth just seems a little different. However, it's very obvious there's a bar at top and bottom where one eye is getting image while the other eye just gets black and it's very uncomfortable on the eyes.
I wish I could share screenshots of this, but as far as I can tell screenshots aren't full res or 3D, and going out to tell it to take a screenshot just shuts the video off completely anyway.