So now that I'm on a Mac, using WinFF isn't quite as handy as it used to be. I was having a great deal of trouble figuring out how to use ffmpeg on OSX until a student in the Flash class, Peter Blaire, found the missing link.
I was using ffmpegX, a shareware utility to convert video using ffmpeg (like WinFF it's a gui front-end). But none of the video was encoding with any meta-data. This is all kinds of bad becasue things like cue points and the total run time are incredibly handy for streaming and vital for publishing the screencasts I do. Aparently you need to install a little ruby on rails app, which you can find instructions on here:
Note that the readme file works better than what you see here, as you need to sudo in the terminal before the install command:
ruby setup.rb config
ruby setup.rb setup
sudo ruby setup.rb install
Works like a charm! Thanks Peter.