I don't understand.

You parented to emitter to the space ship, and then you animated the ship, but the particles don't follow or the emitter doesn't follow? Are you caching them before you animate? If so, turn off the cache. It it's just the emitter that doesn't follow, check to make sure the heirarchy is right, or if you just animated the emitter without using parenting, try re-keying it.

If you want to piost the file I could take a look because it should be easy to do what you want so I bet you missed something really small. Happens to me all the time.