Can I put in a point of view I think is going to get some pretty fierce argument here?
South Africa as a country has some seriously screwed attitudes around sex and sexuality - you are talking about the country which has finally got rid of it's president who was denying HIV/AIDS was a sexually transmitted disease.
From what I have read, Semanya is from a rural area of South Africa - and the chances of her having had more than cursory medical care (vaccinations etc) is highly unlikely. Intersex individuals ARE more frequent in the Southern African communities, but even in the UK approximately 1 in 1000 births will require that some simple examinations are made to work out the actual sex of the infant - but if it was a traditional midwife delivery for Semanya, then this would probably never have been even considered.
In addition, she could have "just appeared" on the SA athletics scene - given a simple time series where she made a local win, then a regional win with a national coaching representative present, she could well have gone on to the world championships in less than a year...we are talking about a country with much less organisation and structure than most european countries.
I still think the IAAF messed up by broadcasting their doubts to the world. SAA officials perhaps SHOULD have suspected the possibility of intersex, but it would be interesting to know what kind of medical expertise their advisors have - after all, there is clearly a LOT of ignorance out there about intersex individuals, as shown up by the various reactions to the news about her.