Popup windows retreat when page changes

Using Lectora 2008, testing in IE and FirefoxI have a Project divided into Chapters and Sections. I have a Section at the end called Popups that has pages for a Glossary, Contacts etc. I setup buttons for each of these that when clicked open the page in a new window such that the user can access the Glossary while the project runs. The project runs in an automated fashion, with markers in the .flv audio files executing a Go to Next Page or Go to Next Section action. Whenever one of these actions executes, the Glossary retreats to behind the new displayed page. I have only tries this in Run Mode and Preview mode, and Preview in Browser, but am worried my published course will do the same, and that users may become confused if the Glossary "Disappears". I spent the last couple hours reading every Glossary and Popup topic I could find, but nothing seems to touch on this, so I thought I would throw up and hand and ask. I used the example "Anatomy of the Human Eye" as the basis for my glossary, and it seems to have similar issues of the glossary retreating to background when the page changes. Many thanks in advance.