I have been with good success, embedding FLVs processed from Quicktime movies for use in self-playing .exe and .app projectors from Flash. However, since I've started using CS5, the FLV video in the movies play back really choppy and aliased. Below are the specs I've been using. Perhaps someone else has run into this?
FLA & FLV animation FPS: 24
Publish Settings: Flash Player 10; ActionScript: 2; Hardware Acceleration: Level 2 - GPU
Compression setting in Adobe Media Encoder: FLV; Bitrate to max 10,000