Screen reader - closing layer problem

Hi. We have courses with popups build as layers. The problem we encounter is related to the behavior of NVDA reader. Everything works great when u vist the slide, open the popup (layer) - base layer is not clickable when the popup is visible. But when the user closes the popup the reader starts to read text on the slide again (on the base layer). Sometimes from the beginning and sometimes if there are more than one popup (layer) on the slide and more than one paragraph on the base layer reads fisrt or with closing the second popup the second paragraph. Focus order is ok on the slide. Can anyone help with this problem?