I am new but, I am guessing that when you use the incorrect '#include "wire.h" you will not be able to write to EEPROM. I am thinking your SD card uses the same pin or interrupt or something along that line.
Post the code and I am sure someone more knowledgeable will help you.
It's obvious about the wire/Wire. It was late!
I'll check out the pinning later today, but at the moment it just looks like the I2C is 4 & 5, and the Wire.h SPI uses 11, 12 & 13 or some such higher ones.
I've got an Ethernet/SD shield arriving today I think. If so I'll trensfer to that and see what happens.