Hm, isn't there anybody how has the same problem? Strange ...
I have the same issue but not just with FLV. It seems to happen on any swf file (apart from the YouTube one that you mentioned). I am still looking for a solution.
Have you tried setting the scale mode to showAll?
This seemed to have fixed the problem for me but I am still testing it out.
thanks for your answer, unfortunately it didn't have an effect on my side ..