Ok, nice to hear that we are not alone
Yes our moodledata directory is on a shared storage (NFS share). Localcachedir and tempdir resides on local filesystem though (not that it should matter).
We did upgrade our moodle platform earlier this summer to 2.8.5+ and at the same time we changed our memcache store to a memcached store instead. However the problem is still there with the muc/config.php being reset now and then.
In some certain situation moodle decides to reset the muc settings. I haven't figured out yet what could be triggering this strange behaviour.