If you suspend a batch and then try to load another transaction or batch and see the error 'Root element is missing', you have a lock on the SEM file associated with your user account.
The lock usually clears itself. If it occurs every time you suspend a batch, the SEM file may be the cause. Contact support quoting 'Root element is missing — SEM file', and include your username and details of when it occurs. If clearing the SEM file does not resolve the issue, the cause may be a KOFAX XML configuration file that cannot be written to and contains no data. Contact support again and they will update your configuration file.