In looking into a StackFlair issue, I have discovered that MSO is not being returned as part of a user's associated accounts. Please see my associated accounts according to the api. Note that there is no mention of a MSO account, however I clearly have one.
I've noticed a lower rep being displayed for a few days, I just hadn't gotten around to looking into what was causing the lower rep display. I'd say it has been like this since at least Friday if that helps any.