Found an answer but hope this doesn't corrupt anything else.
It seems that since in Moodle 2.6 students cannot be actively marked as started on a course, the course completion check for them doesn't start either. See line 50-55 in moodle/completion/cron.php. Deleting the debugging check did the trick.
see also: https://moodle.org/mod/forum/discuss.php?d=267882#p1159172