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.
That sounds like more of a logrotate issue. Take a look at /etc/logrotate.d and see if there's any configuration that would cause that.
If syslog-ng is still appending to the rotated file, then the logrotate configuration for that particular log needs something to tell syslog-ng to start writing to the new file, something like:
in the configuration of the relevant log file rotation.