How can I get perfect synch on exported animation video?

I use CS4 on Windows 7. I have a lot of RAM and a big CPU. And yet, I am having trouble getting the exported video from my animated cartoon FLA to match the good motion/synch on the SWF. The FLA is sized 1920x1080. I have been exporting it down to 640x480 with various export settings for video and sound. The product slows down the motion at early moments like a scene shift tween, while the sound moves along as scheduled. Simply put, I want my MOV file's animation to perfectly match that of the SWF.