Default cwm not backing up all files

I ported 6.0.3.7 to my device and it backs up fine, but when I try to port 6.0.4.8 it misses some files during the backup.

for example, my device does not have the bootanimation in system, its symlinked to another partition from data but cwm ignores the symlink so I just get the generic android logo on boot.

any ideas on how I could fix it or is it that 4.1.2 is not compatible with newer cwm's
Devices I have
Samsung Dart--Samsung Galaxy S3--Samsung Galaxy Note II--Samsung Galaxy Exhibit--Huawei Y301A2--LG Optimus L9--Alcatel Fierce
Asus Transformer TF300--Hisense Sero 7 Pro--Zenithink C71--Teclast P85