Why does Nova Launcher keep resetting my customisation?

After launching certain apps (such as SimCity, Opera Internet or my pic gallery, or sometimes for seemingly no reason at all!) Nova Launcher keeps my home page layout (such as widgets etc) but resets many of my customisations such as grid size, home page transitions, icon theme and app drawer settings...very annoying. When I try restore my back ups it has no effect.

I have tried clearing my app cache, deleting recently installed apps and reinstalling Nova Launcher. This only started happening yesterday after happily using the app for 6 months. I have Prime too if that makes a difference. Oh and I have an unrooted Samsung S3.

Steps so far that I have done: cleared app and phone cache, reinstalled app, reinstalled google play store, deleted recently installed apps...

Thanks so much in advance for any help,

Jimmy