I'm not sure what you mean by "I've exported out to the .SWF (while using loop option)". I guess it the transport control in AE. That won't effect your final render.
Actually once you render your animation, it should play from beginning to the end. So you can loop it like what you want.
Hope this link will help you.
http://aftereffectbasic.blogspot.com/2012/05/tutorial-2-render-or-output-an...