Video switching from interlace to progressive on render

We have a video 29.97 1920x1080i which we are running dynamic linked through after effects, and when we render the video out in premiere it is switching from interlace to progressive.
When the video, in the dynamic link is left un-rendered, we can see the fields in the video, they only disappear after render.
We have tried rendering into several different codecs, ProRes 422 (HQ) being our preferred codec.
Has anyone else experienced something similar?

The issue is present, even on our external monitors. I just had a chat with customer support, it offered little help:
  Ankit Chillar: Please elaborate the issue you are facing.
  Jack Savage: We have interlace media, which we are dynamic linking through after effects, and back in premiere, before we render the clip we can see that it is still interlace, but as soon as we render it, no matter what the codec, it renders into progressive
  Ankit Chillar: What is the version of Premiere Pro and after effects are you using?
  Jack Savage: cc 2014.2
  Ankit Chillar: Hi, Checked this information for you
  Ankit Chillar: After Effects renders the video frame by frame so if you send a project from AE to Premiere then the sequence would be progressive by design and ca not be changed to interlaced
  Jack Savage: why is it not rendering inside of premiere?
  Jack Savage: not using premieres render engine
  Ankit Chillar: because Premiere will treat the file as a uncompressed media file and render it as it is.
  Jack Savage: I would like premiere to operate the same way the AE render engine does, giving me an option to choose the field order.
  Ankit Chillar: I am afraid that is not how the application is designed, If you have suggestions for any improvement or feature you can register your suggestions on following link :0186602810
  Ankit Chillar: https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform
  Jack Savage: we can force it into interlace by changing the setting in modify, is there a way to make that the default setting when using dynamic link projects?
  info: Your chat transcript will be sent to [email protected] at the end of your chat.
  Ankit Chillar: No sir, there is no workflow to do that, However a workaround might be possible for that you can post the query on our community forums. The support staff on forums as well as many of our active professional users might help you with the workflow.
  Jack Savage: ok thanks
  Ankit Chillar: Thank you for contacting Adobe. Good Bye.

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