Well, I came across an intriguing explanation for this in "The Third Choice: Islam, Dhimmitude and Freedom" by Mark Durie. Mark writes:
"The modern distribution of female circumcision among Muslims cannot be explained in terms of geography, nor in terms of pre-existing cultures before the arrival of Islam. The Acehnese in Indonesia were Hindus before converting to Islam, yet they practice female circumcision, while Indian Muslims, who also converted out of Hinduism, do not generally follow the practice. The simple explanation for the distribution of female circumcision among Muslims in the world today is that, while all four schools of Sunni Islam allow the practice, it is only the Shafi‘i school which makes it mandatory. Wherever female circumcision is widely practiced among Muslims, this is a region where the Shafi’i version of Sharia law prevails. In this case it is belief which determines behavior, not perfectly, but to a very significant degree."
I have since had many Muslim acquaintances affirm that many of the differences in the ways Muslims practice Islam can be attributed to different schools of jurisprudence. So there you go.