I've come across this numerous times, and I can certainly tell you what NOT to do - if you're creating a static or spec prototype, it's generally not worth to include any animation, expecially if the file will function as a basis for development. Not only will it confuse the programmers, it makes it almost impossible to use the file as a basis for documentation (say, writing SCRUM stories).
One solution I did try is to show the animation in a storyboard format, but this didn't go down too well with the programming folk, as it confused them even further.
What I would suggest is to keep animated prototypes seperate from the static ones, and simply adding links to an external file in the element description field. This way you'll be able to give one file to the marketing department or the product manager, and the other one to your friendly neighbourhood specifications guy and programmers.