Did you change your Repository settings in the QEMC from XML to SQL Server? If so, it's possible that you didn't migrate your data. You would then need to change the settings back to XML, and redo the transition (this time, making sure to "migrate").
Alternatively, this may be a problem with your config file, especially if you have previously modified it or if you're running multiple servers. Check the file: (your installation directory)/Publisher\Command Center Service\QVPublisherCommandCenterService.exe.config