This is crazy. I gotten this issue no less than 10 times on CM10.2 Maybe I should go up to CM11 again, but 4.4 has so many incompatible apps (easy voice recorder for me).
Nandroid manager doesn't work properly. It says "success" on restroring whatsapp, but doesn'tactually work right, since when I test it by uninstalling whatsapp first, and then restoring using the nandroid manager, it asks me to reverify my number when I open the app. (if it restore properly, it should not ask you to reverify number, like in TitaniumBackup)