I'm running WP 3.9.1 and New Blog Templates 2.6.4.
I've set up a template site which is basically the default blank site you get with WP but with a few additional settings.
When I use this as a template for a new blog the default comment from 'Anonymous' is not copied to the new site.
I have the template site set to copy everything except users (although changing it to copy users makes no difference).
If I go to the post listing in the dashboard of the new site, the 'Hello World' post shows there is one comment, but when you click on the speech bubble to take you to the comments page it says "No comments found."
Having a quick look at the code line 59 of blogtemplatesfiles/copier.php does not tie up with the comment preceding it.