Does it have a preloader? Like loading bar etc, it could be that its not loading fully while hes watching/playing, and its catching up with itsself, if you could upload the Swf file somewhere Like "truploader" and send it to me, i may be able to help ~ Just may be a lil easyer if i can see the scale of the issues.
If it is huge you could make a video file out of it. Flash can be faster than animated gif files because it runs like a movie while different computers will run the same gif file at different speeds, depending how fast the computer is.
That is why a flash movie file works better, but if the frame size is large even movies will take more video speed. More than 640px (high or wide) is large and you need to keep the size under that. Closer to 300px would be best. A FLV file is a good movie file and it will start playing while it is downloading. It needs a player, but you could upload it to Youtube.
If anyone needs a player that plays FLV files the Zoom Player works great. [link] It will play anything.
I use FLV files on my website. I have a player that the script points to with the link to the video.
Shockwave makes a small internet file. SWF stands for Shockwave File, but it can also mean Small Web File. I remember cartoons, games, website buttons with a lot of things that are interactive, and If you use big images, or large files, you can see some of the distortion when Flash downgrades them into a smaller file.
If you are doing you animation is in a SWF file I don't have a clue what it is doing that can use a lot of computer to run it.