Hey enzopalmer, there have been quite a few cases where the render was different from the viewport (and sometimes animation different from single frames).
You should try baking the physics before rendering. Should help a bit.
You might also want to have a look at this post (especially at the bottom): https://blog.cgcookie.com/forums/topic/doing-this-using-physics/
When there are still problems left, please provide us with a link to your .blend file (through Dropbox or whatever cloud service you like).