did you tried my solution above? i am on 3.8.2 and still working fine… Correct time, and format nice to read.
Forgot to mention: Look on file /etc/syslog-ng.conf, inside that file to the part, where you have destination messages {
If you use string which I have,
template("${R_YEAR}-${R_MONTH}-${R_DAY} ${R_HOUR}:${R_MIN}:${R_SEC} ${PRIORITY} ${PROGRAM}[${PID}]: ${MSGONLY}\n"
you should have correct timestamps, I believe. Pity that this is “bug” from default settings. But at least fix is relativelly easy to apply.