I have looked even further into it today, and i still didn't get the SD card to work.
I have come to the conclusion that the W5100 chip may be using pin 9, can anyone please confirm/deny? I think that the schematics are not accurate in this, so Eagle may have to be used.
Schematics: http://dlnmh9ip6v2uc.cloudfront.net/datasheets/Dev/Arduino/Boards/Arduino-Ethernet-v112pg.pdf
Eagle files: http://dlnmh9ip6v2uc.cloudfront.net/datasheets/Dev/Arduino/Boards/Arduino-Ethernet-v11.zip
Thanks!