Adobe Media Encoder

Hi - I have been attempting to use Adobe Media Encoder to encode mpeg-2 files but keep getting the video squished top and bottom, with black bars top and bottom, and a loss of quality. Here's the dilemma:

My editing program exports at 720x486 or 720x480 (whichever I choose) with any avi or QT codec, but when I take that file and use Media Encoder CS4 to make the mpeg-2 to send to station's ftp sites, the file has the previous mentioned issues.

When I change the pixel aspect to square, it works fine, or if I export using the DV type-2 codec it will work fine (the DV codec just doesn't look as good after the mpeg-2 compression is added on). I'm guessing that station's will need standard, non-square pixels though.

My editor works in 720x486 non-square pixels. And I've tried exporting with different codecs I have loaded, such as Uncompressed AVI, NEWTEK 25 AVI, AVID QT, Apple Uncompressed QT, and several others with the same effect when AME is done.

Has anyone come across this before? Or have any solutions/things to try?
Thanks! TC