Don't know if
this is any help or not. I've encoded some video to flash with the on2 encoder and a bit of help from people here but most of it is beyond me so I was just glad when the client was happy and went away.
I did sit through the lady who runs this site's presentation and she sure seemed to know her stuff, some of it really applies to any lossy encoding. She did promise to put here presentation on her web site but it's not there yet, probably have to wait until she gets back to the USA.
One thing she did say that stuck. It's not a trivial task to get good flash encoding. Budget enough time and money to cover spending time optimising the encoding, every video has it's own unique best profile.
Bob.