If surgeon who opened your abdomen and explored the area around and under the bellybutton didn't find anything then it is very hard for me to diagnose your problem. If the cyst wasn't removed completely it may grow up again.
Urachial cyst is remaining from the embryonal structure called urachus which is a communication duct between the bladder and yolk sack during the earlier stages of the embryonic development.
Another cyst-type can remain from an embryonic structure called "ductus omophalo-entericus" which is a communication duct between intestines and yolk sack during the early stages of embryonic development, too.
Both ducts passes trough the umbilicus and they normally disappear in the latter stages of the fetal development so they shouldn't be present when the baby is born. But in rare cases ducts or their remaining (cysts) can stay present in the adult body. If the cyst communicates with the bellybutton there will be discharge coming out from the bellybutton.
I hope that doctors in Boston will help you more.