Oh ok, try this instead:
<?php if($this->countModules('left') || $this->countModules('right')) { ?>
<script type="text/javascript">
setTimeout("s5_load_pos()",1000);
</script>
<?php } ?>
If you have the original problem still try increasing the 1000, to 2000, etc
Ohhh! yes! It works a little slower than the original, but without overlaping :-)