What version of the MRAA library are you using?
If you have issues using SPI with MRAA I'd suggest you to interact directly with the SPI interface from the Linux console using SPIdev. For example in Re: Using spi1 from Linux a user manages to use SPI this way. Some more info about it:
Which version of Edison image are you using? The previous one would not allow the clock faster than 6.25mhz, the new one sort of will. But there is still large gaps of time between SPI byte transfers and really large gaps of time between SPI transfer calls.
Note: with new build, I am also having issue with SPI eating data when there are gaps of time. It appears to be caused by power management changes. I have a hacked up version that is working better.
More details in the thread: SPI (Adafruit 2.8" TFT) not working on R2 Beta - Arduino breakout board
Also some posts showing delays in: http://forums.trossenrobotics.com/showthread.php?7145-Experiment-with-Intel-Edison&p=66508#post66508
not sure what version number. Current beta Intel® Edison Boards and Compute Modules — Software Downloads
I am running modified version
root@edison:~# uname -a
Linux edison 3.10.17-yocto-standard #5 SMP PREEMPT Thu Feb 26 09:25:09 PST 2015 i686 GNU/Linux
posting talking about beta Edison R2 Beta SW Released