Fix sync issue on streams with non-zero start_time

- Apparently the thing to do is adjust presentation time by
  start time so that all streams start at zero. This
  definitely fixes a sync problem I'm seeing (github issue #46
  "Audio delay playing back mp4 files"). Other players
  play these files fine and digging around this appears to
  be the way to deal with it. I'm not a fan of spreading the
  adjustment code all over but the timestamp-to-time conversion
  was already spread out so at least it's not any worse than
  it was before. Just not any better either.
- I'm not totally sure this is the best way to handle it but
  my first stab of adjusting packet pts directly didn't
  work out.