I have an AI file linked into my ID file. The AI file is a header with my contact info and logo, it is used in multiple documents. When I export this one particular document it does not export the logo, only the text. My other documents export just fine and this one has been fine in previous iterations. I am on CS5.
This is one of those "hard to say" problems. Try placing the art again in a new frame -- don't reuse the current frame. Any time I've seen this it usually is something wonk withthe particular frame. Copy/paste a working instance will sometimes work, too.