Video quirky when exported using media converter

Have put together a premiere movie...all ok. then exported in movie converter to flv..then inported into flash...exported and uploaded with dreamweaver file..
on the web am getting jumpy lines as if the compression has gone bad.
Didn't happen the first time with a slightly bigger video but changed and edited to make it smaller...
My question is...is it the process from premiere that is the problem and if so how to fix or has it been corrupted further down the line?

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Eddie
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