Spontaneous perforation of the intestines are known to occur in newborn babies. Some of the common causes such as NEC and HIrschsprung's disease already have been excluded in your case. There are a significant number for which a well defined cause cannot be identified. These perforations are more common in premature babies, babies that are being ventilated or have generalized infection. Fortunately, if they recover from the initial episode, there are usually no long term worries.