Hello,
can you check administrator/components/com_artiofusioncharts/helpers/helper.php
Around line 633 there are these two rows:
$js .= ' chartObj.render("' . $secondaryID . '");' . PHP_EOL;
$js .= ' chartObj.addParam("wmode", "opaque");' . PHP_EOL;
If you have same order of them, then you have change their positions to:
$js .= ' chartObj.addParam("wmode", "opaque");' . PHP_EOL;
$js .= ' chartObj.render("' . $secondaryID . '");' . PHP_EOL;
So param will be added before rendering flash. This missing param make this problems that flash is over everything on your website.