To repeat part of the last post, you must use the new beta version of SdFat if you change the SPI data mode with the SPI library. Each call to SdFat will reinitialize the SPI bus with its mode and speed. You must reset the SPI speed and mode each time your program accesses the SPI bus.
Once again, The Arduino SD library is just a thin wrapper for the SdFat library so SPI behavior of the two libraries is the same.