Try changing the homepage setting by going to Preferences -> Homepage. If you can't find the URLs there, check prefs.js in your profile folder. Unfortunately Firefox may overwrite this setting even without an extension (such as on update) so it is indeed better to use favorites instead of the text field :(

There isn't an explicit warning on install because the purpose of the speed dial is to change those pages, but I will try to make it clearer in the description. Thanks for the suggestion!