Are you perhaps working in DV25? In which case your resulting file is not squashed to 4:3; it is squashed to 3:2.
Professional tools such as After Effects, do not seem to set display flags for DV aspect ratio, either because that is a relatively new QuickTime feature, or because quite frankly, they don't need to. They are set up internally to render to the correct pixel positions and squash (if 16:9) or stretch (if 4:3) your video to fit the 720x480 DV25 frame. What you are seeing when you play back in QuickTime Player is the actual pixels that make up the video clip. The display is wrong, but that's the actual pixels in your movie. If you import that clip back into, say, Media Composer or Final Cut, you would then tell your editing software what aspect ratio you are working with, and it would handle it correctly. In Media Composer, for instance, aspect ratio flags are routinely ignored, and everything displays in whatever format you have selected...and it's up to the editor to stretch, squeeze, or mask the video if it was shot or created in the wrong aspect ratio. That's why AE doesn't set the display size; it knows you're probably going to go back to something else that is going to handle the video as native pixels anyway.
In QuickTime Pro, you can set the display aspect ratio manually. Use Window|Show Movie Properties (j), select the video track, select the Visual Settings tab, UNCHECK the "Preserve Aspect Ratio" box, and manually enter the square pixel size into the "Scaled Size" box. Save the movie, and it will "remember" the new size. When you compress the movie for web display, export it to a proper-ratio native size rather than as the raw DV stream.
Oh, for NTSC, the screen dimensions to use are as follows:
When starting with 720x480 DV25...
...scale 4:3 video to 640x480
...scale 16:9 video to 853x480
When preparing non-interlaced graphic materials to use in DV...
...create 4:3 material at 720x540
...create 16:9 material at 853x480
--Dave Althoff, Jr.