Very nice board ;-)
As a workaround, you could use software SPI instead of hardware SPI. Unfortunately you'd need to re-route the SPI connections to different pins, as the hardware SPI pins can't be switched to GPIO because SPI is needed for accessing the flash. For SW SPI just load the spi-gpio-custom module for example like:# bus<Y>=<devid>,<SCK>,<MOSI>,<MISO>,<mode>,<speedInHz>,<CS> insmod spi-gpio-custom bus0=1,1,2,3,0,100000,0
After this, you have a 100kHz SPI bus at /dev/spidev1.0 using GPIO0..3 for CS/SCK/MOSI/MISO in that order. For the mode parameter, see spi.h. I'm using this in several Omega2 based projects successfully.