I noticed some odd behavior in that the last-input-event is mouse-2 whether I press mouse-1 or mouse-2 when clicking on a link. It is also interesting the event is of type mouse-2, and not down-mouse-2.
Does anyone know if org-mode makes a mouse-1 click into a mouse-2 event somehow? Is that happening from this line
(org-defkey org-mouse-map [mouse-2] 'org-open-at-mouse)