Ok, I've tried several different roms and I always back up. I've used Oudhs, Clocworkmod and TWRP. No matter which one I back up with I never have any luck on restore. They all seem to restore ok but I get stuck in boot loops everytime. Factory reset doesn't help. Wiping caches don't help. This is just beginning to really drive me nuts. I don't really mind having to reinstall everything but jeez I just wish I knew what the deal was. I never had trouble on my Motorola Defy or my Galaxy S2 but I sure can't seem to get anywhere on the S4
I use OUDHs Touch recovery v1.0.3.3 in conjunction with Rom Manager and I have NEVER had that problem. Also, when I use Rom Manager to "Back Up Current Rom" I can NAME the backup file, and it goes into the recovery and uses the filename I have already typed in and it's a seamless operation. Even using restore via Rom Manager works seamlessly and it has NEVER balked on me.
The only time I had a problem was once using My Backup Pro and trying to do an on-line system backup. MMS, SMS, Call Log has always been absolutely perfect! No out of sequence messages, and all the pictures are restored correctly too!
Aloha and Good Luck!
BTW, I am on a Stock 4.2.2 with the latest M919UVUFNB4 (modem.bin) Flashed for the radio and it's reception qualities are better than it's ever been before!