Comments do not display after permalink changes.

Hi there can you help good people ? I have latest WP and Atahualpa versions. In WP I changed permalinks from "default" to "post name". After this change when I click on "x comments" to see comments, they do not show at all. When I change back to "default" permalinks it works fine. Please help as my site was hacked week ago. I did not have comprehensive backups so I spent a lot of time polishing it back to the old stated and I lost already lots of clients because of that. So your quick help will be much appreciated.