Yes, that's exactly what I mean - you must embed the font outlines. Naturally, to save on size you might want to selectively embed only those characters you are sure you will be using. Use the "generate size report" feature to verify your resulting swf.
By the way, system fonts extending beyond the confines of a scrollpane is not necessarily an error. Though it may appear this way in the authoring environment, often times it plays fine a browser. This is due to a bug in the flash player release which was ultimately corrected (with version 6.2 , I believe - check Macromedia to be sure). If it is not critical that the fonts be "crisp", embedding will guarantee correct playback regardless of the player version (embedded fonts are automatically antialiased, which, for small font sizes - below 12pts, can actually decrease readability.