To verify that the channels are equal, connect the output left channel to input left channel. Do the same with the right channel by connecting the output right channel to input right channel.
You should also make sure that the volumes are set equal for both channels. If not, the frequency response will not be centered at 0 dB but will have an offset that is determined by the volume difference.
Test and set the levels from Measurement->Test Levels. Adjust the volumes if required. The input signals for both channels should be equal and in the range –30 to –3 dBFS.
Start the measurement from Measurement->Start. You should now see a flat magnitude frequency response as shown in the figure below.
The Time Data plot should show the value 1 at the first sample and very near the value 0 at the other samples. If you change the vertical axis from Linear to dB, you will see a noise floor that should be around –100 dB as shown in the figure below.