You published your flash swf with 100%, publish it whatever sizes you have on the stage. Change your settings in the publish settings dialog to publish the files within the specified dimension.
I did what you said, but it made the movie worse instead of better. Some of the arrows disappeared completely. So I took a look at my library,& found the "SM skem2.ai" file. I thought I would be able to edit the Illustrator file, but instead, it took me to a file with all my movie clip instances on it. (if you downloaded the native flash file, take a look in the library & you'll see what I mean)
Long story short, I fixed the temperature arrows, but now my return arrow (the dark red one that moves along the top pipe back into the pool) isn't moving. If I try to re-animate it, then the temperature arrows go off the stage again!
Is it because they are the same movie clip? I can re-import that clip with a new name if you think that will fix it.
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Revert the file and Just apply a mask on layer