I just got a GTC 980 TI OC version installed and the game is amazingly smooth all over with DK2. 3D is perfect, but for me too the problems come when SC:ing closer to a planet/station. Glad to hear 1.5 is working better and the issue is addressed.
Edit: The issue is with headtracking in SC. After a 20sec or so, the judder begins when moving your head, usually when heading for station. Otherwise everything is A ok.
I think if you'd check your frame rate you'd see that it's dropping to around 50 or so. VR needs a steady 75. So you're probably always getting it in SC but it's just more noticeable when you move your head.