Ghosting/blurring in FLV files

Hi all,
I have built some pretty long timeline animations that I am exporting as .mov files and then converting to .flv.
My quicktime settings from flash are all set right up high so the final .mov files are very high quality. I then run them through Adobe Media Encoder CS4 to create my flvs with and alpha channel.
I have run this process with 45 different files (some several times as amends are made) and the results have always been fine but after the last round of amends one file is coming out with ghosting and tracers on all the movement. Other files under the same profiles look fine and the mov for the problem one looks fine also.
I have tried encoding on different machines (Mac and PC) with many different settings and while the results are different each time they always contain this ghosting effect.
The files are built mostly of png files being transitioned around the stage. They are long (up to 4000 frames) but all are very similar so why this one should be causing problems is puzzling.
Anyone have any insights in to encode settings either in flash or Media Encoder that might help to fix this issue.
Thanks alot

It is the same file. One thing that might be a factor - I encode in Mpeg4 which is the only section of Sorenson that seems to deliver the H.264 codec. This produces .f4v files which, because of the way my site has been designed (not by me) I have to re name .flv  Not sure if that is relevant. How do the videos look to you? as I say - they play totally smooth on my Mac book pro.  Should I try a different codec. I would happily drop some picture quality if I could get the motion smoother. I am encoding 2 pass vbr with a max bit rate of about 1300Kbps.  Thanks for your help. Nick

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