I am not sure whether this problem has been resolved in a later release or not but this is what I came across yesterday when working on a clients blog yesterday. I thought it appropriate to share this observation with the community so that if it had not been taken care it should be now.
I changed the wp-config.php file to a new database [by exporting the database and then importing it to the new database, with a different table prefix say fswy_ instead of the default wp_] the widgets in the sidebar got broken.
When I observed and investigated the issue I figured it out that the option value for the that the s:19 [s:19:"fswy_inactive_widgets"] was incorrect and have to fix it manually to make it like s:21 to restore the broken widgets.
Hope this will help the community to fix or at least look into this to see if this still remains something to be fixed or was just a one off incidence.