So I have a simple flash movie.
I have created 3 layers (actions, background, header) Background contains an image, header contains a movie clip with an instance name of "mc_header". In the actions layer I have said mc_header.visible = false; Yet when testing the movie it continues to show for no reason.
The way you say this it should work. Post a link to the source file...
Are you sure when you say "instance" are you referring to the name of the layer or the actual name of the movie clip? From the question and description this seems like it might be a valid point.
Another problem could be if you are doing a timeline animation and using keyframes. If the movie clip is not present (on the timeline and stage) when you call the actionscript then the action is not performed.
It might be faster if you just provide the source files so we could help you faster.
Cheers!