I had the same issue with loosing resolution in output files, and here is my story:
Upgrade both Premiere and Media Encoder to latest versions, and render with MAXIMUM RENDER QUALITY….
When exporting progressive footage from Premiere to Media Encoder Yu MUST make custom SEQUENCE which is PROGRESSIVE (NO FIELDS), because if you export progressive footage from default interlaced sequence, this thing with deinterlacing is happening….
Try, and you will see a big difference…..
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