I have clean install of Alfresco 4.0.0c (3979).
I have created a site and chosen a 3-column layout. I have also added some dashlets (Site Calendar, Site Profile, Site Activities, Site Members and Site Links).
Now - when I click on "Customize Dashboard" button - I see my three-column layout - but every column is empty, so I can't delete any dashlet from my site.
Although the columns are presented as empty - the dashlets exists on the site.
Jakub Sanecki