Ok graicas, Cristian_cena, mi problema se soluciono al poner wmode en la etiqueta embed
Código HTML:
<div id="header">
</div>
<div id="header2">
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0" width="985" height="110">
<param name="movie" value="./tema/online/swf/cabecera.swf" />
<param name="quality" value="high" />
<param name="wmode" value="transparent" />
<embed src="./tema/online/swf/cabecera.swf" wmode="transparent" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" width="985" height="110"></embed>
</object>
</div>