AccidentalTuner Plugin Adjusting Extra Notes

Hi, I have just installed the AccidentalTuner plugin and placing the specified quarter tone accidentals and applying tunings is working for the most part, but extra notes are being changed. In the attached screenshot, I have a measure of the half sharp notes followed by a measure of natural notes. The problem seems to be when I don't have any selections and say "Apply Tunings" in the GUI and then play the score, the first two notes of the second bar are also raised a quarter step. Where can I look to find out what is causing this problem and fix it so the "Apply Tunings" button works correctly?