Some pages in a package deployed to the author instance aren't accessible in the right pane. However, they're listed in the left pane of the site administration tab.
Make sure that you properly install your template/CSD packages before you install any content packages. You can check the status of the affected page/tree via CQDE or toolbox in the contentbus view.
The left side of the administration window shows nodes recognized in the system. The right side shows valid content pages only. The most likely cause is that you have installed a content package that contains pages for which the CSD is not present.