Make sure that both your object and embed tag have wmode set to transparent:
Add in this language to your object/embed tag -
Add the following parameter to the OBJECT tag:
<param name="wmode" value="transparent">
Add the following attribute to the EMBED tag:
wmode="transparent"
Or, if you are using two object tags, as can and is sometimes done, add the param tag to both of them.
If you are using script to generate the tags (as is frequently done to avoid the 'click to activate' feature in some browsers), the wmode transparent must be passed to the script. This is easily accomplished but, varies depending upon the sort of script one uses. Some scripts do it automatically.
There could also be other problems (like z-index, the Flash's source code, etc.), but you must have the wmode set to transparent (as outlined above) to have any hope of covering Flash.