You may have set certain bookmarks to open in the sidebar :

In the Library (Ctrl + Shift + b) you can click on the 'More' button at the bottom of the page. Make sure that "Load this bookmark in the sidebar" is not selected.

In case you use a mouse - it's also available if you: • right-click the bookmark on the Bookmarks menu or Bookmarks toolbar • click Properties • then look to the bottom of the Properties dialog for the checkbox

If that's not it, you could try this : Rename or remove the xulstore.json file in the Firefox profile folder : Go to the 3-bar menu => Help (at the bottom) => Troubleshooting Information. Under 'Application Basics' : Scroll down to 'Profile Folder' and click on 'Open Folder'.

Is the Bookmarks sidebar open in the main window or in another window?

The sidebar setting is a global setting, so if the sidebar is open in another window then the sidebar will open in a new window. There is no way to prevent this as far as I know.

If that didn't apply then rename/remove xulstore.json and if present delete localstore.rdf in the Firefox profile folder with Firefox closed.

You can use the button on the "Help -> Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page.

• Help -> Troubleshooting Information -> Profile Directory:
  Windows: Show Folder; Linux: Open Directory; Mac: Show in Finder
• http://kb.mozillazine.org/Profile_folder_-_Firefox