Could it be pregnancy, or just a hormonal problem?

I have been on the birth control pill, on and off, for about three years now. I have been a little forgetful with the pill, but we have absolutely never done it without a condom. I have never missed more than two pills at once and always follow the directions for missed pills. Since I've been on birth control, my period has been like clockwork. Then a few months ago, I started to feel peculiar. I had weight gain/bloating, but much more severe than usual. I had cravings and had to urinate frequently, and working in a restaurant I was almost always nauseated. My period finally arrived, two weeks late, and then I couldn't get it to stop. I had already taken two HPTs, several days apart, and got a negative on both. After my period should've come and gone the second time (about 6 weeks of non-stop bleeding) I went to the doctor. She prescribed a hormone pill and instructed me to quit taking my BC pill until I was done with the prescription she had written. She tested for pregnancy and the result was negative... My period is late again this time, only about 5 days so far, but I have had no signs of discharge or blood-- only cramping and bloating. I know that I have gained weight, but I just figured that was due to unhealthy eating habits. Could it be a pregnancy, even though the three tests in the past month and a half said otherwise? If not, what could be causing this?