Some tips:
Don't set alpha to 0, instead use the visible property, setting movieclip.visible = false will make it a lot more efficient.
As for the importing and quality, after you import to stage or library, bring up the library (ctrl + l), and right click on the file you imported, go to properties. If it's an image, set compression to lossless, and allow smoothing.
For audio, go to file-> publish settings, and change audio stream and audio event (whichever you might use) to 128kbps.
As for your main question, I need more info, if you want you can post your source. It might be because of how you are placing your graphics on the stage.