Maybe its an issue with the SD board. Do you have two SPI devices in your project? If so the issue is with the SD cards/boards.
I found the SD Cards (including Sparkfun and AdaFruit) do not tristate the MISO pin of the SD board.
More detailed explanation:
ON every SPI slave board (ie any SPI sensor or SD or RTC etc) should "disconnect" the MISO pin when CS tells the SD board to not use the bus. However the SD board does not "release" the MISO pin so it remains an output when the processor is trying to talk to other SPI devices.