It sounds like you are in a frustrating position and I can understand why you feel the way you do. I don't think you are mad at all. There are many possible explanations for what you are going through. Having a long term girlfriend that is supportive and open to talking about things is fantastic.
When the thoughts started was there any event that might have occurred around the same time? For example did you have an argument with someone, or was some sort of negative comment made? Sometimes the smallest thing we pay no attention to can get stuck in our head and our subconscious tries to work it out in various ways.
Is it possible that there is a part of you that wants to speak to your Dad about it? Have you ever tried talking to your parents about your sexuality? Sometimes when we keep something important from people we care about it can manifest itself in different ways. That might be why it is happening after three years of you being out.
It is also possible the more you try and fight the thoughts the more dominant they become. A sort of self-fulfilling prophecy where you don't want to think about it, so you do.
If the thoughts become too overwhelming, or frustrating for you to deal with there is always the option of reaching out to a counsellor. There is no need to think yourself mad, and there is nothing wrong with getting alternate perspectives. You are most definitely not alone, and there are others who may be able to shed some light on your situation. They will also be able to offer or help you learn healthy ways to deal with or handle these uncomfortable thoughts.
Suzanne at AlterHeros