Don't know what to tell you. I just made a quick test.

MovieClip symbol of a box rotating (used a tween) over 20 frames.
Main timeline 2 frames.

The square keeps rotating like it should. I thought maybe you were having a
problem with stop() or the maintimeline restarting, but in my case it didn't
matter if there was a stop on frame 2 or not. Everything kept playing.

But if I put a stop on frame 2 and then change my instance of the spinning
square to a graphic?well then it stops as soon as the main timeline stops.
Remember just because something is a movieclip in the library doesn't mean that
you haven't somehow accidentally changed the instance on the stage with the
properties panel.

Other than that, there must be something about your structure that you aren't
clearly explaining that makes it behave differently.