Stenis hade lösningen. Men jag hittade den innan på en engelskspråkig sida, tyvärr kan jag inte nu hitta adressen. Men följande kopierade jag från sidan.
When you click the Favorites menu in Internet Explorer you find that all of your favorite URLs may be missing. This might happen if the Favorites Shell Folder is set incorrectly.
How To Solve:-
Start>Run>Regedit>Ok
Now navigate to the following keys:-
[HKEY CURRENT USERSoftwareMicrosoftWindowsCurrentVersionExplorerUser Shell Folders]
Set the Favorites path to : %USERPROFILE%Favorites
[HKEY CURRENT USERSoftwareMicrosoftWindowsCurrentVersionExplorerShell Folders]
In the right-pane, set the Favorites path to : C:Documents and SettingsUsernameFavorites
Where Username is the current user profile name.
Jag ändrade i registret och nu fungerar åter mina bookmarks.