The Astigmatism program runs single-pass time of 30 minutes. Typical run time is 120 passes, so this would be 60 hours. It is possible that they were irritated and painful from the action of the program. It may have been killing some pathogen or detoxing and causing the irritation. It is good to stop programs at the start of irritation / symptoms, wait for them to settle down, then continue until the 120 passes.
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