After Sha Dow Wiz Ard's comment on his question I'm wondering if this is intended behaviour. When I received new answers on an Area51 discussion question and a Stack Overflow question I was alerted in both the inbox tab and the notifications tab of the Super Collider.
For other questions on other sites, this hasn't been the case:
And also:
It only seems to have happened for those two answers, I can't tell if it's cause they're slightly older or if it's related to the site that they are on - any ideas?