Hi there,
Just like Jakub said before, you will need to configure the option
"leave-msg-on-server" to "false" in the pop-client section on the Email Server application in CME. Aditionally, you may set the log level to debug on the Email Server component AND in the pop-client so that when the next pop-cycle will happen you may see in the logs of Email Server what is actually going on.
Please make sure that the username that you use in the "mailbox" option of that pop-client HAS the right to delete emails from your Corporate Email Server.