Deinterlacing BMD DNxHD footage

I am currently running 1080i footage through a BlackMagic ATEM Television Studio, and taking 1080i output into a BlackMagic HyperDeck Shuttle 2 via SDI, which is set to record to a Quicktime DNxHD format.
Unfortunately, if I edit this footage in Premiere Pro CS6 (using the mac version FWIW), I can not for the life of me get it to deinterlace.
I've tried setting the Field Options on each clip to "Always Deinterlace."  I've tried exporting to explicitly progressive settings.  I've checked the "Render at Maximum Quality" box when rendering.
If I run the raw footage directly through Handbrake and set to Deinterlace there, it comes out right.  If I run the final Premiere Pro footage through Handbrake and set to Deinterlace, it comes out right.  I just want to know why all of the settings in Premiere Pro designed to convert interlaced content to progressive content are failing to do their job.
Am I missing something?
Thanks for your help.

Step 1:
Export video to YouTube 1080p settings (or manual H.264 settings with 1080p output).
Step 2:
View video.  Observe interlacing lines everywhere.
Step 3:
Turn on deinterlace filter in VLC.  Interlacing lines disappear.
This would be one example of the non-deinterlaced output, which is pretty evident the minute you turn on 1080 streaming:
https://www.youtube.com/watch?v=uaWVvv40kaw
I suppose it's possible the Premiere is doing some deinterlacing, but doing a phenomenally poor job of it.

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