And as someone else said - you're crossing your eyes, when you should perhaps be doing the opposite - looking far into the distance until the images overlap.
I always wondered after seeing this a bit ago if the addition of a torso might also help. Part of the disorientation might be that it seems like your body is not there. A nose with a torso and eventually LeapMotion like hand controls/arms, may help reduce VR sickness.
As far as why it looked flat rather than inside out, I can only guess that that depth info conflicted with the other depth information you get from vision (parallax, known relative object sizes, perspective lines) and my brain ignored it.
EDIT: Actually, after trying the second view (the one with hands, not the roller coaster) cross-eyed, I saw the inside-out depth. It's most noticeable looking out the window.