If you import a large PNG with no alpha you will have slower frame rates than importing the same images as a JPG even at 100% compression, regardless of the Flash export settings for that image. You could set the PNG to export as an 80% JPG and it will still perform worse than if you imported a 100% JPG to begin with.

The hows and whys are interesting to know, but irrelevant. Your animations will slow down if Flash has to deal with a larger source file. I've done my own testing and have proven it to be true. Since I can't depend on the end user having a great video card, it's more important to maximize performance across the board by importing 100% JPGs when transparent PNGs are not necessary.
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