CrossRoads:
"The SD library has its own pin mapping tables, for the ATmega1284 it assumes the Sanguino pin mapping. "
So as long as you keep SS, MOSI, MISO,SCK as D10, 11,12,13, there is no problem.
Are you sure? Your Bobuino_directions.doc file states: "And finally download & install the SdFat library
http://code.google.com/p/sdfatlib/downloads/detail?name=sdfatlib20110702.zip&can=2&q=
and use this file C:\Arduino-0022\libraries\SdFat\Sd2PinMap.h". Your Bobuino17.zip file contains a modified Sd2PinMap.h file with a Bobuino-specific mapping. Maybe you've forgotten about these changes?
Actually I made a mistake in my post, I used the '644 initially and the SD library does assume the Sanguino mapping in this case. There's no specific mapping in Sd2PinMap.h for the ATmega1284, it falls back to using the mapping for the ATmega328, ie SPI on D10-D13 (ie PORTB2-PORTB5). The ATmega1284 needs PORTB4-PORTB7.
Either way some modification to SD/utility/Sd2PinMap.h is needed.