application run by service and user run simultaniously, update failsAnswered

I have an application that starts once an hour from a service. That same application can be run as an exe. The application uses the AutomaticUpdater control. When I publish an update with wyBuild and the user restarts the application the AutomaticUpdater control starts updating, but then the Files in use… dialog comes up. It states that the AutomaticUpdater.dll is in use and it must be closed before the update can continue. Clicking Close Process or Close All Processes doesn't do anything. The only option is to Cancel Update. I assume the service is running the application and the updater can't close it. What can I do to make it work?