You need to bypass the plugin every time you are exporting audio from your DAW. Otherwise, the correction will be applied to your master bus mixdown. Note that the plug-in is meant to calibrate your speakers and room just like acoustic treatment would. Failing to bypass the effect would mean adding the sonic anomalies of your system to the rendered audio.
Make sure you make a full plugin bypass in your DAW, not just the calibration bypass inside your Reference plugin.
We have also introduced a render bypass notification system that currently works on selected DAWs.
You can read more about it here.