I presume this is SD source? Sequence settings?
More info like this will help others to help you.
I would try the following with a 60 second section of your final sequence.
Export a Quicktime movie(self-contained) of your sequence.
Open with Quicktime and if it displays correctly in QT take that into Compressor and use the presets to create an MPG-2 and AC3 file of your movie.
If the aspect ratio is still wrong:
On a older version of QT and Final Cut we used to have issues with QT displaying the FC exports correctly even though it was 16x9 in Final Cut.
If this is SD 16x9 you can also change how it displays in QT.
Apple+J/video track/visual settings/uncheck preserve aspect ratio and change size to 853x480 and save. The movie should now play nice with Compressor SD settings.