I have cut together footage from the Canon 5D Mark II and set up the project with the appropriate DLSR pre-sets in Premiere CS5. I'm attempting to render out the finished cut using the Vimeo HD presets , however, the rendered mp4 file has two major issues: (1) All the transitions (cross dissolves, fades, etc) have simply disappeared and there's a slight drift in the audio near the end of the video. I haven't encountered these two issues in a very long time...what have I forgotten to do?

Try to encode again to see if the problem repeats.