I wondered about the steps that were given, and so tried turning on advanced layers before pasting the layers, and the animation worked ok. But then I realized what had made it work. As I suspect was the case with Nitin, I happened to make a new HTML5 Canvas FLA, that I pasted into. So I tried again, with AS3, and the problem was still there.
You can take your original file and do a File/Convert To/HTML5 Canvas, and the new FLA will animate correctly in a browser. If you went on to do an export video, the video is ok too, even though it goes through a making SWF stage, and making SWF from AS3 still shows the problem.
I found that even converting an animation to frame by frame doesn't solve the problem, which also means it's possible to isolate a single frame of a single layer, to show the problem.
nitins41702265 , try this zip, it only has a single frame of the bush in its ending position, as AS3 and as HTML5 Canvas:
http://colin.scienceninja.com/justbush.zip
Test Movie both of them, and you'll see the bush is in the right place for HTML5 Canvas, and the wrong place for AS3.
The bush doesn't have any sort of 3D transform on it, in fact the only thing in the scene that does is the river reflection, but the bush test FLA doesn't have that. I haven't yet figured out if there is a way to remove 3D transforms from the entire file, and converting to html5 and back again isn't enough to solve the problem.