Are you seeing the NACK's while using the EV2400 or your uC? I have verified that these parameters can be changed using the EV2400. If you are seeing NACK's while using this interface, then your device may be damaged. But, I would think that all it would NACK all communications. If you are having problems while using your uC, then you are going to have to compare waveforms between the EV2400 and your uC to see what is causing the problem.
One other thing to check first is that the device will not allow you to update some parameters with Impedance Track enabled. You can export a gg file, set Update Status to 0 and import the gg file back into the device. Press the Write All button to transfer it to flash. This will disable IT.