One idea: we should have a look at mlogger::close_channels(). There the SYSTEM buffer is emptied through the cm_yield() call. Instrumenting this with some debugging code will enlighten us. 

Another possible problem: If the frontend requested to be notified for a run stop AFTER the logger, then the problem might happen: Logger closes file, and THEN the frontend flushes events ending up in the SYSTEM buffer and being logged at the beginning of the next run. The mfe.cxx framework takes care of this by calling 

cm_register_transition(TR_SOP, 500);

while the mlogger does 

cm_register_transition(TR_STOP, tr_stop, 800);

and since 800 > 500 the logger will be called AFTER the frontend. If one use a framework different from mfe.cxx, this could however be different.

Stefan