FWIW I do not see this issue on the latest version of org on the master (dev) branch.
Based on the backtrace, it looks like for some reason comment-start-skip is nil in your emacs session.
(defun org-agenda-skip ()
"Throw to `:skip' in places that should be skipped.
Also moves point to the end of the skipped region, so that search can
continue from there."
(let ((p (point-at-bol)) to)
(save-excursion (goto-char p) (looking-at comment-start-skip))
(and org-agenda-skip-archived-trees (not org-agenda-archives-mode)
(get-text-property p :org-archived)
(get-text-property p :org-comment)
(and (setq to (or (org-agenda-skip-eval org-agenda-skip-function-global)
(throw :skip t))))
Can you recreate this error in an emacs -Q session with only that org version loaded?
Trying again since it wasn't received the first time.
Ever since updating to 20160801, I've encountered the following error
whenever trying to run org-agenda-list: