Eu respondo a mim mesmo. No final, houve algum problema / bug com o kernel. Eu atualizei para o kernel 4 e tudo deu certo novamente!
$ sudo mount -t cifs -o credential=/root/.smbcred,vers=1.0,rw,uid=1009,hard,nosetuids,noperm,sec=ntlm //[MyDomain]/centren /media/S
[sudo] password for myuser:
$ ls -la /media/S/AG/[MyAG]
insgesamt 196
drwxr-xr-x 2 myuser myuser 4096 Jan 8 2016 .
drwxr-xr-x 2 myuser myuser 196608 Feb 9 15:30 ..
drwxr-xr-x 2 myuser myuser 0 Feb 12 10:03 MyDir
$ uname -r
4.4.0-98-generic
$ mount.cifs -V
mount.cifs version: 6.0
$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.5 LTS"