Adobe Media Encoder wont preserve widescreen

I have a mp4 file that has a resolution of 640 x 360 pixels.
When viewed in VLC it looks natural and in proportion. I simply
want to convert the .mp4 file to an .flv file for web distribution
maintaining the existing dimensions. I am attempting to do this
with Adobe Media Encoder.
The problem is that Adobe Media Encoder insists on converting
the file to a 4:3 aspect ratio with a resolution of 480x360 pixels.
Viewing the output in VLC results in a squashed out of proportion
image. The output preview in Adobe Media Encoder also looks
squashed.
When I select the option to specify the output dimensions and
manually set the resolution back to 640x360, in then adds to solid
black bars on the right and left-hand sides of the video which is
undesirable - aswell as making the video squashed. I have messed
around with every setting and have had no joy in producing the
output I require.
I have a command line version of ffmpeg which is able to
convert the video successfully (keeping the correct aspect ratio)
using the most basic command: ffmpeg -i input.mp4 output.flv . I
don't want to resort to using ffmpeg at this point. I just spent
$1200 AU to upgrade to CS4 Design Premium and want to use the nice
GUI I just paid for :)
Any help would be appreciated. Has anyone has a similar
problem with AME CS4 (I found at least one instance on the web)?
IMO it is a bug with the software - or a limitation, please tell me
I am wrong!

I am having the same problem, with the same dimensions - 640x360, coming from a very high quality .avi, and not matter how I tweak the settings AME insists on crushing the width down to what appears to be the standard 582px. What gives? I haven't seen any answers to this yet...

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