Exporting HD file to an .flv, aspect ratio is off

I am trying to export from FCE a .mov file and transform it into an .flv for upload on a newspaper website (the only file type our creaky admin alllows). The footage was shot with a Canon Vixia HD AVCHD camera and brought into FCE at 1440 X 1080 and 29.97 fps. My usual workflow is to export it out as a master .mov vile and then take it into Streamclip or iSkysoft Video Converter and transform it into an .flv.
But every time I do it, no matter what settings I tinker with, the output .flv file is clipped and footage on the screen is clipped on the right and left sides.Is it because HD video is 16:9 and the .flv size is 4:3? But I am only being offered 480-320, 640-480 and 1280-720 in export options for .flv with iSkysoft and frame rates from 20, 24, 12 an keep original frame rate. Tried these all and still getting the clippings.
Any advice as once again I run up against the shoals of transcoding?
Douglas

I finally had to export the file as an .avi and then transcode it into an .flv using Flash Media Encoder, an old workflow and which produced a video with some artifacts and color issues. I am just getting used to shooting with the Canon Vixia and its HD files and any tips for outputting to better quality with an .flv format is most welcome:
Here it is: http://wvgazette.com/News/201107171218
Douglas

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