ok seem to have an answer for this.
For some reason playing an embedded movie in Unity suffers this problem, which appears to be more a case of a long delay, meaning the first few seconds are missed, rather than any codec issue.
Playing the same movie via WWW using a local file does not have this problem, it plays instantly, has no black frames and doesn't cut off the first few seconds.
My assumption is that when playing the embedded version it must be loading the entire movie or a considerable part of it into memory before playing. This means when it does start playing it has to skip forward a few seconds to be in sync.
I'd say this is a bit of abug as clearly WWW verison plays fine.
For reference I used the answer to this question.