First question I have is, "Do you have a good install of the ROM from the beginning?" If not, then that is the problem. Verify MD5sum is good. I have backed up and restored this ROM multiple times after trying other ROMs. I use Philz 6.48.4 and wipe davlik, wipe cache and wipe all to install new ROM. This last step will format system, data and cache. In Backup, I pick the ROM to restore. Say "YES" to restore. Wait 2 minutes until done and reboot. I also wipe davlik and cache PRIOR to doing Backup. Makes them smaller and the restore doesn't take as long or puts junk back that I don't want.
I've even restored a stock 4.1.2 with no problems. I use the latest Clockwork which i recently found out has issues duplicating root folders.
I don't think it's the recovery tho cause I've restored a bunch of different roms without issue.
So I'll give the md5 a check.
Thanks for the heads up.