Clips Appear From "Nowhere" After Save

Holy bleedin' crap, I'm about to throw my system down the stairs -- this is driving me NUTS! Here's the deal:
I have hours and hours of raw footage in iMovie. I've gone through each clip and edited-out portions I don't want. I drag my clips tot he timeline to start building the main movie, and after a while, I save.
Then it happens: clips suddenly appear in the Clip Pane -- clips that are old, etc.
WHY IS THIS HAPPENING?!? Is it because I tried to edit clips while they were in the Pane rather than after they were in the Timeline? It's totally screwing up my movie, because I think I'm almost done with a section so I save, and then clips appear from footage that should have been included in an already timeline-added part of the movie.

Is the project saved on an external drive? If so, and if the drive does not use the Mac OS Extended disk format, iMovie can't reliably save to the drive. So when you try to save, nothing works as it should.
Karl

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