make the flash file so that it doesn't run automatically..
then put OnLoad="runflash();" in your body tag..
and put this somewhere in your page
Code:
<script languae="Javascript">
<!--
function runflash() {
document.getElementById("movie_id").Play();
}
// -->
</script>
Where it says "movie_id" you have to change it to be the same object id as your flash movie has in the html document.