I occasionally experience the same thing. When this happens, it appears the jwt token is not sent with the initial request (thus appearing to be logged out), but it is sent with api requests on the same page (unread_count, list, etc.), so the cookie is not lost (document.cookie also shows it). Sometimes refreshing again fixes it, but I haven’t yet found a good workaround. I’ll experiment a bit next time it happens.
Cataclysm: Dark Days Ahead