Right click on the domain in GPOADmin and then go to "Re-configure Version Control server". If you are using AD then you can select another domain controller for that server to connect to, likely one that is closer to the server. If using AD LDS or SQL, then the store may be too far or the link may be too slow between the two servers.
If there are a lot of registered objects within the version control root it is highly recommended to use a local AD LDS instance or SQL Server to store the configuration. If the product is currently using AD it is possible to migrate the configuration to AD LDS or SQL Server. Please contact support at 1-800-306-9329 to assist with the migration.