Edit. Seems resolved.
New Kinja Issue? Maybe! The notifications all link to the local area you are in. For instance, my notifications are, from my drop down while I am at my personal kinja home are:
When they should be (as taken from my notifications page):
I didn't see this one specifically addressed in the kinja help tag... so I figured I would report it. It takes on whatever kinja area you are on, so one click will get you to the article and then reselecting the notification from the drop down will get you to the specific area/comment.