As of now, with ST3 Build 3126 I am still experiencing this issue (or designed behavior...).
When using toggle comment on a mixed selection, only the non-blank lines are commented.
Used on only blank lines, these lines are commented.
To me, this behavior is rather un-intuitive, but I guess a matter of taste.
For some "languages" or file formats, though, this is really an issue because blank lines can change the interpretation of files in certain programs (I a specifically talking about FEM solvers like LS-Dyna).
I would really like to see an option which can control that behavior.
The most elegant way I think to control this would be through an option for the
Comments.tmPreferences file (similar to the
This way the behavior can easily be changed for different language/file syntaxes.