Well, do you have Final Cut, I think you can export from there.
I would suggest you export your animations to a good Quicktime Codec like Animation or for smaller file sizes, Photo-JPG At 100 percent.
These files then can be transcoded in final cut or in encore with great results.
Sorenson 3 is a delivery format much like mpg-2, you don’t want to every cross transcode these end formats. Stay with a high quality or uncompressed format until you are ready to publish.
Good luck,