This new version is a considerable improvement over an already invaluable tool. It's faster and more reliable (I was able to transcode videos that crashed the older version).
The only problem I've found is quite annoying, though: when re-encoding an mp4 movie that refused to play on my AppleTV (instead of using the preset when encoding the DVD, I tried to make it higher quality. Serves me right), it did a great job, but doubled the length of the movie, adding blank space to the end. My 3-hour movie shows up as a 6-hour movie. It did not increase the file size. This has happened to 3 movies now - always double the original. Note: only when re-encoding an mp4.