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ffmpeg tends to break a lot with respect to ratio/fps, usually with propietary formats (WMV) created by broken hw/sw (cameras, windows encoders of questionable quality..)
as you've said, it all comes down to what is specified in the container (RIFF or whatever) and what the actual data (WMV3) tells, it should be the same which it isn't and ffmpeg gets confused.
if you really want to use ffmpeg, the solution is to manually specify -aspect or -fps with ffmpeg and check the result if it plays ok.
finally, jwplayer is probably to blame because it ignores the aspect ratio specified in the flv metadata. you must stretch the video to correct aspect ratio for flv playback, or fix your flv player.
however, when dealing with variety of formats i recommend you vlc/mencoder, which are much more smart about detecting these defects - after all, software dedicated to playback is bound to cope with broken stuff better.
also post questions like that in webmasters Q&A, this section is just too spammy :)
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