You had mentioned the issue coming in preview of topic, does the same issue occur when you generate the output and view the topic.
Also is the issue coming with this project only or did you try creating a new project and adding popup in that project and see if every thing works fine.
Yes, the same issue occurs when generating the output and viewing the topic. I should note that the project is using a template that was created in RH7. When importing that template as a "Master Page" and starting from scratch in a new project, the issue does not appear to occur.
I did also notice that links to bookmarks within other topics do not work correctly in the upgraded project. The bookmarks are present and the highlighted text is still linked to the bookmark but when previewing (or reviewing in the final output) the link brings up the start of the topic containing the bookmark, not the text that has been bookmarked. Each link has to be redefined in order to work properly.
Thanks for your help!