Changes made manually on the about:newtab page are stored in the browser.newtabpage.pinned (default = [null]) and browser.newtabpage.blocked prefs that you can check/modify on the about:config page

• http://kb.mozillazine.org/about:config

This somehow fixed itself after a couple of days of unpinning. I'm not sure what I did but if it comes back I will try your method. I just had a look in the about:config page and couldn't find either browser.newtabpage.pinned, nor browser.newtabpage.blocked, but that may be because I no longer have anything pinned. Thank you.

Yes, those prefs are only there if you have either pinned or blocked an item on the about:newtab page.

If it happens again and you do not keep changes after a restart then see:

• http://kb.mozillazine.org/Preferences_not_saved