I'm not sure if what you are experiencing is the same thing but I have seen flash videos on sites do similar things. In those cases that I have seen the fix was a combination of css and an extra parameter for the video.
For the css you should check the positioning of the div for you spry and also the movie, if one is relative and the other absolute you can get some issues like this. The other css thing to check is the z-index, if the positioning for the objects is the same then the z-index will dictate their stacking order.
The other part is an attribute for the objects params. If you have the wmode attribute present or available make sure it is set to transparent. Like I said I have only seen this with Flash videos but the result of it seems similar to what you are describing.
