Xperia V require root permissions every time
So here is what I did:
First I tried Bin4ry method's from XDA
with the 3rd option, it installs Superuser, but its buggy and it doesn't remember the permissions.

So then I did it with Motochopper method from XDA 
which installs SuperSU, and the root apps now require permissions from SuperSU just once, and it's working fine. 

After that I safely deleted Superuser.