I would recommend you back to see your PCP. It sounds unlikely that you are pregnant due to the negative results and the fact you were on birth control. However, as nothing short of abstinence is full proof and tests have been known to show false results, there is still the slightest possibility. Your doctor should be able to get a definitive answer for you.
Missing your period could be down to any number of other factors; stress, being under or overweight, a change in medication or even a change in schedule can throw your body off.
Pregnancy aside, the fact your body is displaying symptoms irregular to you, is reason enough to and get checked out.