Importing FLV to flash

Ok I love the way CS4 has a nice media converter so you can instanly import FLV files but what I have recently found is that the voice of my videos all go out of sync when inputted into flash but are fine if I play then direct from my hard drive. If I import the file in CS3 and convert them directly in CS3 then the voices are all fine. Because i’m using many transparent .png images I have to use CS4 because CS3 adds a nice jagged edge when these are rotated. Any idea why i am having issues with audio for my videos in CS4, some settings I have to place when converting or in CS4?