I recently prepared several videos for a website. I exported them from Final Cut Pro using Apple Compressor. They were encoded using H.264 and originally fast start streaming (though I ended up trying the other streaming options as well).
When the webdesigner loaded them into the flash player, and you pressed play, the video would immediately skip ahead 4 seconds and start playing normally. I have no idea why. I tried every possible option (different streaming options, different key frame settings, etc). Nothing worked.
The webdesigner tried exporting from Quicktime Pro, enabling hinted streaming. It worked. I tried the exact same procedure with the exact same settings and it did not work, the videos still skipped ahead.
In addition, a couple of the videos also had sync problems. However, if you seek ahead in the video it immediately syncs up correctly.