To keep video and audio in sync you're relying on sample-perfect decoding and this can go wrong very often (think audio interface does not support 44.1kHz sample rate for instance, true story from Creative Labs). To avoid this, older codecs used to feature audio/video interleaving, so the relevant audio went hand in hand with the relevant video. You can notice this on older divx videos that tend to skip a frame every so often. Newer containers such as Quicktime/h264 have a timebase parameter so it's no problem to sync things.
So when transcoding your video, the following could go wrong:
- It was wrongly encoded at the source. Say your encoder component was a bit off. Adobe tend to cause this often.
- It was wrongly decoded for the purposes of transcoding. Say your codec component was exotic so the video host's one got things wrong (happens to a lot of opensource).
- The transcoded video was then wrongly decoded by your computer. This does not necessarily mean it would happen (or not) on other computers. It's not entirely predictable.
- Everything is fine at source, transcoding, and decoding, but the hardware is locked at a different sample rate. No way to predict what's going to happen if your player/component/OS does not cater for this. OSX does, to my awareness.
Things to try:
- Try the other "quality" settings (480p, 720p).
- Restart your browser.
- Reupload in a super-common format: mpeg4 h264 48khz stereo and cross your fingers.
(They did sound different to me so it might be the third option you're heading towards. Also consider the "internet weather" sometimes causing SNAFUs even on the biggest sites.)
Hope this helps.