Hi guys, I work on a MAC and use Final Cut Express for all of my movie editing. Sorry I can't help more with the window side of things.
I always export out image sequences, too, instead of a pre-compressed movie. Other than giving me more editing options, image sequences are nice when SU crashes during export and you can start exporting from the last rendered scene transition instead of having to start over.
I use PNG as it is uncompressed and the files are small in size.
I also try to avoid materials with lots of contrast as high contrast textures also flicker and flash during playback. I will sometimes go so far as to edit a desired material in photoshop to minimize contrast. Groundcover textures are particularly troublesome, in my experience.