Scanning the AD
Number of processed servers during the scan is incorrect.
The problem may appear when scanning a certain Organizational Unit(OU). For example if you have an OU named SharePointFarm with 7 SharePoint servers, but a SQL server is located in another OU. The message during the scan will say: "Processed: x out of 7 servers." While in fact the number of discovered servers will be 8 (because of the SQL server).
After the discovery process is finished go to the Alerts tab -> click Manage. Locate the Farm in which you have missing servers -> click Add Server and manually add the missing server. You will need to provide a Server Name and a Server Role(s). For more information on how to do this see this article.