It is not OK for a patient to have sinus congestion for an entire year. It is not normal for a patient to develop a recurring fever for a day or two almost every month. When these symptoms occur simultaneously with the onset of joint pain, maybe there is something actually wrong with your patient. I don't know, maybe your patient is actually ill? Running a gamut of tests that return negative results and then telling your patient, that it is just her allergies, is not proper patient care. She has had her allergies for her entire life and she has only had the aforementioned symptoms for the past year. Something doesn't add up here.
I think doctors should be comfortable with saying that they do not know what is going on. Referring a patient to a different specialist or to another colleague for a second opinion doesn't mean you are a bad physician; it just means you want someone with a different perspective and a different set of experiences to take a look at your patient and help you figure out the problem. That is how medicine is supposed to be practiced.
Maybe you're right, maybe her allergies have just progressed and the symptoms have become worse over the past year. Even if that is the case, you should probably tell your patient why you are not modifying her allergy medication and its dose because, otherwise, it seems like you are saying her allergies are getting worse and she just has to live with that. Maybe that is also true, and there is nothing medicine can do for her new symptoms, but TELL her that, don't make her guess. I feel like I'm just asking for basic patient care that every physician should provide...it seems to ME like all of this is just common sense.
In the end, your patient is confused, suffering, and thinks her doctor is incompetent and a bit of a jerk (the latter two points may or may not be true...I have no idea, I've never met you). She is so desperate for decent medical advice she has resorted to asking a first year student what she should do and then exclaimed that I gave her better advice than you ever did. That is embarrassing. Relatively speaking, that is like a dog providing better relationship advice than your best friend...seriously, us first years are idiots (for now...).