I do not have the solution, but I did run into a problem several years ago when we migrated a windows file share to the a netapp running 8.1 or 8.2. I do not remember the fix but we certainly saw the slow directory listing, I do not recall if I was seeing the permission denied. Sorry I am not more help but our desktop guys resolved it on the client, it may have been something with local cache settings or something. Sorry again for the lack of information, but I though knowing there is likely a client side resolution may be of some help.