When linking directly to the Comment Reply form using the #respond anchor (e.g., http://raamdev.com/2014/make-excuses-or-make-it-work/#respond), the padding around the Comment Reply form is missing:
The issue here is that the CSS only applies the padding to #commentform-top and #commentform-bottom but when linking directly to the Comment Reply form the form does not get placed in either of those divs.
The solution is to apply the CSS formatting to #respond. Note that it will be necessary to retest the new CSS changes with the reply form that gets loaded when replying to threaded comments.
Fix comment form bugs when using comment reply links. See #68.
Fixed in master branch. Will go out with next update.