Do you have your naval pierced?
Have you tried talking to your doctor yet? I had a similar problem, and she told me it could be ingrown hairs. Along the belly button is where your pants rub, so it's not uncommon. I was told to hold steril gause soaked in warm water to the area to open it out, then try to "pop" them.
However, mine keep coming back, and I have liver problems, so I need to look more in to it. But the above is what I would try first, if I were you.
hope this helps :)
I believe it is just a little infection. If you have an "inny" belly button, then water sweat or what ever can get stuck in there. Where there is a moist, warm area there is going to be bacteria. But a little Neosporin(triple antibiotic cream) in there and in a couple of days it will be better.