Don't run the sp/dif direct from the input jack of the BNC direct to the input of the DAC chip. Run the BNC to the network on the board. In other words, hook up the jack connection as you would stock. Then jump out the selector switch. 75 ohm cable should be used for all connections. At 24/96 and above, impedance and shielding are very critical.
If you still have problems, you can send the unit to me, but be aware I have five EE DACs waiting for mods right now.