Hello Yoshi,
Thank you for your post.
I've reproduced the same issue with some our MOV files. We will try to fix it in the near future.
As soon as the udated version will be ready, we will post it here.
According the second issue with MP4 rotate flag, could you please uplaod for us the sample input file with such flag to any file host service, e.g. Google drive or Dropbox.com to reproduce the issue at our end?