I was having problems with clamav after install. Out of date errors, and unable to update errors. I disabled clamav by commenting out the call to it in /etc/amavis/conf.d/15-av_scanners while I try to get everything working.
This might be the reason for the disappaering messages. Please undo your changes and fix the problem as described in the ISPConfig FAQ:
Then send a message from an external source and post the lines that get added to the mail log when the email arrives at your server.