The Primal Blueprint is not a magic cure for everything. If you have a chronic medical condition the PB will probably help, but it might not fix it entirely. You sound like you are doing the diet pretty well--keep at it, but understand that it might not make you 100% all the time.
Also, how is your sleep in general? Are you taking vitamin D or getting LOTS of midday sun? How is your stress? Are you exercising at all? All of these things are part of the PB and they all affect immunity to some degree.