Working with 16x9 footage

I am wondering if anyone else is encountering this issue. Much of our footage is shot in 16x9, AVCHD that is transcoded to Apple Pro Res to edit in Final Cut as an HD project. (Some of our cameras don't do 4x3 at all)

However, when we use the settings recommended for ACM standards MPEG2 compliance using Apple Compressor the footage looks distorted (stretched). We tried to change the settings in Compressor to accommodate for letterbox but then the video file is not seen in our server (a Leightronix Ultra Nexus). Maybe it is us.

If we convert the files to an SD sequence the project will export as an mpeg with substantive image quality reduction.

I don't think our playback server is the issue per se (we've got a query out to them, too), but one of more broadly working with 16x9 native footage and trying to spit it out for ACM Server compliance.

Does anyone have any experience with anamorphic wonkiness and interlace issues on 16x9 compressed Mpeg-2 transport streams?

Thanks,
Jason