When I first went to MF9 from rooted, stock rom MDL, I did my restore with TWRP Nandroid backup. It worked, but I ended up with odd issues. Apps closing, phone would reboot on its own, sometimes twice in a row, etc. After a half day of that, I went back to stock MDL, reinstalled MF9 stock, rooted and did the recovery via TiBu. Worked very well, even restored all my Nova Launcher settings. Very little additional setup after that. A couple of shortcuts, etc. Been rock steady for several weeks on MF9, stock rom, rooted.
I think the nandroid backup has some system level stuff that makes it unstable when restoring on a new firmware. It works great on the same level, though. I could be wrong about that too, but that is my impression.