Folks, we have seen where Site lists are visible under the PWA Quick Launch Bar. This occurs when an admin changes the PWA configuration (well this is actually in the SharePoint configuration). In Project Server 2007 you can access this on Site Actions > Navigation (Under Look and Feel). This will bring you to Project Web Access > Site Settings > Modify Navigation.
Once on the page, look at the Global Navigation and confirm your checkboxes.
Recommendation to do any changes on your TEST system BEFORE making changes in your Production system.