Just lost days trying to resolve a problem with this combination.
Shoot was 24P, D800 hdmi set to 1080i (didn't know about the hdmi to auto trick yet for real 24p out). Expected to get normal pulldown. Logging footage I was getting strange interlace artifacts at a funky cadence and nothing could,resolve it.. Working with Avid MC6, FCP7, Cinema tools, Aftereffects. Finally ID'd the problem...
D800 output was PsF with 2:2:2:4 pulldown..
Problem was that the Shuttle2 captured the PsF stream with the wrong field dominance, so only 1 frame in 5 (the doubled frame) was whole.
Solution was two passes through JES Deinterlacer (awesome tool).
Pass one: Switch field dominance.
Pass two: Skip every 5th frame.
Unfortunately, we had to make 2 passes as we couldn't find a way to change the order of operations in JES. We used uncompressed or DNxHD 220x as intermediate files depending upon take length. I was pleasantly surprised that even after 2 extra runs through the DNxHd codec, the quality was still great.
Now, if the Shuttle just wouldn't ALWAYS capture 16 audio tracks to QuickTime files even only Two are are in use. My Avid Media Files folder has thousands of empty MXF audio files now.
thanks, this is a great help on the way to getting the best from the HDS II and Nikon d800 combo. Through your post I have discovered JES, which seems to be a godsend to this problem and many others I'm sure.
Jes doesnt find the frames to skip, so I don't know if you would be able to say more of how exactly you have set this up.
I should say that since your initial post the HDS II firmware has been updated to include the Apple Prores HQ codec option which I have been using. So perhaps this codec isnt falible to the 5th frame skip problem. But it definitely still shows the interlacing issues, which seems to have been cured by changing the field dominance via JES as per your suggestion.