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Also, I should note that I have run the latest updates for both Premiere and Media Encoder.
If you have all of the updates and still have the issue, take special care in Media Encoder that you have all of the correct settings selected before exporting. I say this because, I had the cropping issue when a widescreen sequence would default to 4x3 in Media Encoder (which I missed and didn't change to widescreen) resulting in a cropped, reduced size video that took forever to export.
I don't know what you mean by 'take special care in Media Encoder...' - I'm talking about having trouble with Media Encoder. I can't take special care because it isn't responding to what I want to do.
I think what Charles means is that generally you set your export up in PP which then sends it to media encoder. However media encoder doesn't always get it right so you need to double-check all of the settings again in media encoder. Hope that helps!
I'm getting the problems while still in PP, though (as illustrated by the pics I posted).
Well, I've figured out a work-around for now...
It seems that PPro is having trouble nesting a 1080p sequence inside a 720p sequence and/or outputting a 1080p sequence to to anything other than full 1080p or 720p with anamorphic pixels at 960x720 (instead of 1280x720). I don't get it, but I found a way to get what I need... it just takes a while.
I was able to export my film to 720p H264 with anamorphic pixels. I then made a new project with a 720p sequence setting and dropped in my newly encoded 720p video. With the new project I was able to export the 720p video to any format I wanted without any of these cropping issues.
I'd still love to know what causes this.