I noticed that in opencart 126.96.36.199 the order confirmation for admin contains the comments from the user, and the email that the user gets doesn't. The user gets only the text version with the comment, not the HTML version with the comment.
In 2012 2013 the problem was that the comment wasn't passed at all into the emails.
It seems the problem was solved only partially.
The solution is here:
https://stackoverflow.com/questions/451 ... opencart-2
EDIT: Has this issue been resolved in OC 3.x?