Annotations sit on top of regular text when flattened

Ever since the new design, some of my annotations aren’t sitting above the text that I’m marking; instead, the annotations are right on the text, interfering with what I’m trying to correct. It looks normal while I’m working on my document, but when I flatten the document, the annotations have moved. I tried adjusting the line height, but that only helps sometimes.
Is there anything else I can do to ensure my annotations look right, no matter which reader someone is using to view the document?