Sometimes syslog-ng will change from logging to the file messages to filename with timestamp appended like this messages.yyyymmddhhmm. Of course this then breaks anything I have that is reviewing incoming logs in messages.
This on Ubuntu 10.04.3 LTS and syslog-ng 3.1.2-1~lucid1. Had same issue on syslog-ng 2.0.9-4.2.