If you use POP3 to read your emails from your maildatabase on a IBM Lotus Domino Server, everything works fine, unless you use DWA too. Emails you read using DWA do not download to your POP3 mail application.

This is due to the fact that DWA removes the unread flag for that document.
To circumvence this behaviour there is an notes.ini parameter that may help. Use the following console command to set it:
SET CONFIG POP3_READ_ALL=1