Delete the menuhax stuff off the root and try to reinstall that. What CIA installer are you using? And ya legit cias don't count as bought. If it is from the actual 3ds than it does. So say you bought a system and it came with pokemin y. Once you sign in it adds it to your account as if you bought it. Legit cias installed with a CIA installer won't do that.
I will try to delete the menuhax stuff and see how it goes.
As for the installer, I am using FBl.
By "sign in" are you referring to that new system Nintendo has with the ID thing or whatever?
Because I used the eShop a couple of times, but that was before that came out.
