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If the Exchange Server Toolbox does not see any emails, it is usually because the Exchange Agents are having a problem (assuming the service is running normally and there are no errors in the Event Viewer).
The first thing to check is whether the Exchange Server Toolbox agents are installed:
First check if the Add-In is listed under Deactivated Add-Ins
Check if the Add-In is inactive
Open powershell and type: Set-ReceiveConnector -identity "<IDENTITY>" -MaxInboundConnection 20
The MaxInboundConnection parameter specifies the maximum number of inbound connections that this "Receive Connector" serves at the same time. The default value is 5000. The valid input range for this parameter is 1 to 2147483647. To disable the inbound connection limit on a "Receive Connector", enter a value of unlimited.
Open powershell and type: Set-ReceiveConnector -identity "<IDENTITY>" -MaxInboundConnectionPerSource 10
This parameter specifies the maximum number of inbound connections that this "Receive Connector" serves at the same time from a single IP address. The default value is 100. The valid input range for this parameter is 1 to 10000. To disable the inbound connection per source limit on a "Receive Connector" enter a value of unlimited.
The signaturs of ClamAV are updated automatically every 3 hours by the "Exchange Server Toolbox" service.
You may trigger an update manually in "Exchange Server Toolbox" in "Anti Virus Options".
The "Exchange Server Toolbox" considers all user mailboxes on the exchange server but without room and device mailboxes.
Please goto "About" page in ExchangeServerToolbox to see how many mailboxes are available.
You can identify which and how many mailboxes the "Exchange Server Toolbox" considers by sending an Lightweight Directory Access Protocol (LDAP) query.
To do so, open "Active Directory users and computers" on the server and right-click on your domain. Select find from the context menu and select "Custom Search" in the "Find:" drop down option.
There you have to select the Advanced tab, paste the following query into the "Enter LDAP query:" field and press Find Now:
Current category: Exchange Server Toolbox