R2 Arduino Uno and an R3 Ethernet Shield mismatch
When I take a look at the schematic for R3,



it appears that the extra pins at the top left:




carry the same signal as pin A4 (AD4/SDA) and pin A5 (AD5/SCL). 

The extra two pins at the bottom left are respectively unused and attached to +5V according to the same schematic diagram. Unsure why the printing IOREF on the PCB gives other impression.



As a solution, you should be able to simply wire the top left two connections to the bottom right ones (A4 and A5). 

A multimeter should be able to confirm my theory. The new connections on R3 have probably been introduced to allow for smaller shields still using power supply and I2C bus.

As a reference the R2 looks like this: