Hi,
The problem is caused by some of your components' router file that overwrites the $config variable when it's loaded.
Thank you for the report, we'll handle this in next version of JoomSEF.
In the meantime, open the Manage Extensions page in JoomSEF and check the components that use "Component's Router" as an Active Handler. Try to switch them to "Don't SEF" one by one to see which one is causing the problem.