I experienced the same thing a few days ago
What I did was incorporate the image I wanted the Flash file to be underneath *into* the movie on the top-most layer, then added a keyframe on that layer all the way to the end of the movie. That way the image stayed in the same place the entire time. After that, I positioned the flash movie using "style=margin-left:210px" so the top-layer image was in the exact same spot as where it would of been if the Flash wasn't even there.
example -> http://www.fogu.com/hm4/test.php
The tree top is only a static image for about 210 pixils. After that, the rest of it (the orange guy in the leaves) is all done in Flash. Flash compression makes that portion of the tree top a *little* blurry, but anyone I've talked to said that they don't notice it.