Reference correction plug-in must be the last plugin on your output. Keep it on your master output as the last plugin.
Remember that the plug-in must be bypassed 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.