I have encountered that problem.. Heres how i solved it...
Never use absolute references on a movie you will be loading from a host movie, like root.whatever, since when you are loading the movie within another movie the root reference you put on the second movie refers now to the host movie.. try to use
relative references like this.whatever or just "whatever".
or you can use absolute references on the movie that you are loading inside another movie but you must include the name of
the empty movie clip that you will be loading the second movie clip into. for example on the host movie you will be loading the second movie on an empty movie clip name "placeholder". so on the second movie clip all you absolute reference must be changed to _root.placeholder.whatever. If you compile just the second movie you can see anything... but if you compile the second first(dont mind the errors and thae fact that it wont work) and them compile the first. Surely it will work..
Hope this helps...