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:

1. Open the Exchange Management Shell
2. Enter the command "Get-TransportAgent"
3. There should be a list on which 2 Exchange Server Toolbox agents appear
4. If that is not the case the easiest way is to reinstall the program
5. If reinstalling does not fix this issue you can try to install the agents manually:
1. Open a command prompt with admin rights
2. Run "C:\Program Files (x86)\JAM Software\Exchange Server Toolbox\bin\ESTAgentExchange.exe" /install (Pre 6.0 ESTAgentNet4.exe /install)

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First check if the Add-In is listed under Deactivated Add-Ins

1. If this is the case select "Deactivated Elements" in the combobox below and press "Go".
2. Remove the Add-In from the list.

Check if the Add-In is inactive

1. Select "COM-Add-Ins" in the combobox and press "Go".
2. Activate the Add-In by checking the box next to its name.

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"MaxInboundConnection":
  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.
https://www.jam-software.com/redirects/?receive_connector

 "MaxInboundConnectionPerSource":
  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.
https://www.jam-software.com/redirects/?receive_connector

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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".

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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:

(&(objectClass=user)(objectCategory=person)(mailNickname=*)(|(homeMDB=*)(msExchHomeServerName=*))(!(name=SystemMailbox{*))(!(name=CAS_{*))(!(name=HealthMailbox*))(msExchUserAccountControl=0)(!userAccountControl:1.2.840.113556.1.4.803:=2))

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