The only way it plays smooth out of flash professional is when it is published as an .html
You don`t publish a flash movie to html, html is only the wrapper around the swf-file, so if your swf works fine embedded inside an html and is choppy when testing as a standalone swf, it has probably to do with some background processes flash is running during the test (Auto-saving or whatever). Try to close the FlashPro IDE before running your swf file, you should get at least the performance that you get inside a browser.
How do you close the the FlashPro IDE? Another thing, I used a macbook pro to create the flash project and I emailed my .swf to my pc and it plays perfectly. On my pc I converted the .swf to a .mov and put it back on the macbook and it plays jerky through quicktime and imovie on the macbook. Seems really strange.
Actually, the pc created .mov plays fine through quicktime on the mac, but when I import it into imovie to add sound effects, it plays jerky like the flash versions.