Possibly an opcache issue:
https://moodle.org/mod/forum/discuss.php?d=337499&parent=1360479
https://tracker.moodle.org/browse/MDL-51376
https://moodle.org/mod/forum/discuss.php?d=244509&parent=1060940
I would agree - I've seen several such redeclare error issues lately on more than one site and they were all related to opcache issues not permissions issues.