Hello,
Thank you for your interest in our product Code Compare.
Unfortunately, we cannot reproduce the issue on our side. Kindly provide us with a screenshot showing your settings where you have enabled the feature to ignore comments. Please provide the information in the request on our helpdesk via this link 
https://www.devart.com/company/contactf ... odecompare
Thank you for your interest in our product.
Best wishes,
Devart Team