I found the problem and it is a bug. I had no idea about the following code found  on UserSettings.ascx.vb:

            UserSettings.LocalResourceFile = Me.LocalResourceFile
            UserSettings.DataSource = UserModuleBase.GetSettings(New Hashtable(Me.Settings))
            UserSettings.CustomEditors = editors
            UserSettings.Visibility = visibility
            UserSettings.DataBind()

As I explained before (many other posts) FCKeditor provider stores its custom configurations inside the tabmodulesettings table for instance and module, and inside hostsettings for portal wide custom settings. So, when a module is deletes, its tabmodulessettings is deleted too.

The code shown avobe takes all key,value pairs from the user accounts module and show them inside its page.

The main problem with the profile module is that it does not have a tabmoduleId, so I was using the User Accounts Module for that case.

It looks that I have to look into another place to store data when no tabmoduleid is in place.

B.T.W. You can delete those values from the tabmodulesettings table. They will be re-generated once a custom fck settings are applied to a fck instance inside the profile module