On the schematic, pin 129 is labelled 100M. In the verilog sdk/src/spi_pwm.v, a comment for the clk signal says "100MHz clock input".
In the pin configuration file sdk/src/mystorm.pcf, a comment for clk/129 says "Onboard 12Mhz oscillator".
When I route the clk signal to a PI_GPIO pin with a verilog assign, my oscilloscope tells me that it's ticking at 33.33 MHz. Looking at Olimex pin 6 also confirms 33.33 MHz.