Not quite sure if I really hit the sweet spot with this solution but thought it worth sharing the experience.
We have seen Compact logging just to the server console and the text log, but not into log.nsf. It didn’t matter whether it has been started by Program Doc, from server console or notes.ini.
I compared notes.ini settings, directory and monitoring setup. I finally arrived at the Log Filters in events4.nsf.
Logging worked on the server where there were NO Log Filters. On the other server, there were log filters. So I deleted them and after a short while -tada- , compact log entries started to appear again. So, careful, those filters do have some global effects.