I've got a little question i couldn't find the answer too so maybe someone here can help:
For imported bitmaps, you can set the "allow smoothing" option so if you dynamically change the x or y coordinates off your image, it will look smooth instead of quircky.
For .flv i couldn't find this option, which results in pixelized motion.
Does anyone know if there is a way to allow .flv to smooth? (other then exporting the whole flv as a bitmap sequence)
Inside the Flash Video Encoder you do not get too many options. If you get a more advanced encoder like Episode or Squeeze, there are many more options for fine tuning your FLV. If you are getting some strobing, check your frame rate, does the FLV match the SWF? Does the video strobe/flicker in the raw video clip? If so you may need to add some post frame blending or motion blur. I use RevisionFX ReelSmartMotionBlur for this all the time.
Also, is your data rate of the FLV low enough that your machine can play it back smoothly? I would guess that it is but you never know.
HTH, if you have any other questions or more info to share, post back here