Do they have a specific reason to suspect Congenital Adrenal Hyperplasia? There are multiple causes for intersex, many which could result in ambiguous sex characteristics.
Its also noted in that article that he was born with some type of anomaly, or 'debility' and that caused him to be baptized in the home, which would be unusual for Catholic families in Poland.
Interestingly, this article on poles.org was written long ago in 2008 and leaked the detail (about this CAH theory) about Gen. Pulaski possibly being a girl. This was supposed to be a secret by the Smithsonian-funded group performing the forensic anthropology analysis and only released now.
This article claims scientists analysed the bones a while back and suspected they belonged to a female, but the DNA evidence was iffy. This was a new study that build on the old hypothesis.