I am having an Identical issue. The help files show an ability to export to EPS 3.0, but there is absolutely no way to do this in Flash CS4 that I can see. For now, I downloaded the trial of illustrator to use as a work around. Interestingly, you have to export from flash as an *.ai file, open it in illustrator, and THEN save as EPS from illustrator. WWWW TTTTT FFFFF. Is adobe deteriorating? I can't even copy from flash and paste into Illustrator.
Perhaps adobe has some kind of explanation - but I doubt it.
As an update - you can export the image as usual, but instead of just entering the name of the file, include the ".eps" at the end. Regardless of the image type selected, it appears to save a genuine *.eps file. The resultant file even worked LaTeX, and I tried it twice. However, you cannot choose to save a "with preview" *.eps file as stated in the help file. I still don't feel bad about what I said earlier...
As a side note - in order to get the EPS to be more compatible with LaTeX, you must break apart all text and images.