QuickTime Pro will do this for you. However, at least in my experience, the converted file loses all of its interactivity. I know QuickTime supports interactive movies; I have no idea how to export something to this format, though. If you help me, you'll be helping the original poster too.
Flash source files are .FLAs, - the outputted files are .SWFs. It's highly unlikely that you will be able to open an .SWF in Flash and export it as a Quicktime movie without any problems (but give it a try-Flash has SOME ability to read back in .SWF files). If you had a source FLA file, you could easily export it directly from flash as a quicktime movie.