Hi simonorangecat, Please check your preferences to make sure they are still the way they are. The most visited tiles on the newtab page do in fact keep track of top sites.

In order to delete the history you can select the option to delete history on exit. If this does not help there is also a places.sqlite file in your profile that can be deleted.

Please also check to make sure the preferences are saving correctly: How to fix preferences that won't save

Is this about bookmarks on the Bookmarks Toolbar?

Make sure that toolbars like the "Bookmarks Toolbar" are visible.

• "3-bar" Firefox menu button > Customize > Show/Hide Toolbars
• View > Toolbars
  Tap the Alt key or press F10 to show the Menu Bar
• Right-click empty toolbar area

Open the Customize window and set which toolbar items to display.

• "3-bar" Firefox menu button > Customize

• check that "Bookmarks Toolbar items" is on the Bookmarks Toolbar
• if "Bookmarks Toolbar items" is not on the Bookmarks Toolbar then drag it back from the Customize palette into the Customize window to the Bookmarks Toolbar

• if missing items are in the Customize palette then drag them back from the Customize window on the toolbar
• if you do not see an item on a toolbar and in the Customize palette then click the "Restore Defaults" button to restore the default toolbar setup

You can check for problems with the places.sqlite database file in the Firefox profile folder.

• http://kb.mozillazine.org/Bookmarks_history_and_toolbar_buttons_not_working_-_Firefox
• https://support.mozilla.org/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file

• Places Maintenance: https://addons.mozilla.org/firefox/addon/places-maintenance/