I suspect a case of intergenomic conflict and sexual antagonism.
Most people, scientists included, have pretty much assumed that genes and chromosomes work together for the good of the organism. Evolution works through cooperative mechanisms---survival of the fittest. Some have put forth the idea that it's actually an interlocus contest between the X and the Y driving evolution with the Y, becoming ever smaller to "hide" from it's oversized opponent. It's actually been called "Evolution: the four billion year war" with sexually antagonistic genes, which benefit when in one gender, but harm in the other gender. Females with 2 X's are at an advantage, males disadvanted by only 1. One example of this battle is the DAX gene on the X and the SYR gene on the Y(makes males into males). People born w/2 DAX genes but are XY, develop into females (rare mutation). It turns out 1 SYR can defeat 1 DAX, but 2 DAX genes defeat one SYR.
To cope with it's aggressive partner, the Y has shed most of it's genes (to lessen the attention of the X). The SYR gene has a powerful arsenal though, and is no victim. Although there seems to be no variation among humanity in the SYR gene, it seems to be the fastest evolving gene, and is vastly different in humans than other primates (10 times different than other genes we share w/primates). Occasionally, the X zeroes in on proteins on the current SYR gene, and there is a collective sweep in which all humanity switches to the rare mutant SYR, which the X doesn't recognize.
I'm getting all this from "Genome: The Autobiography of a Species in 23 Chapters" by Matt Ridley...a book I highly recommend as a fun read, and full of interesting facts. Reading the chapter "Conflict", which covers this idea of intergenomic conflict...it seems the X is sitting there next to the Y (in males) oblivious to the Y's existence, which is exactly what the Y wants. It's scary to think our genome is working this way, but why else would Ryukyu spiny rat, a mammal switch to such a way to make males? Either the X finally won...or the Y found the ultimate way to outsmart the X--join it!