After two days without my phone trying to sort the same problem. In desperation I wiped the user data etc again with CWM recovery but then went on and reformated the partitions with CWM. I then reinstalled the rom (Belgian NE6 KK) and to my surprise no errors and an uneventful boot up with the new rom. Phew!
Device:Galaxy S4 mini i9195 8gb
Rom:Stock Rooted + Wanam Xposed
Recovery:Towelroot/ or CWM 220.127.116.11