Just wanted to say, I figured it out.
I had been migrating from another site. It was another folder on the same VPS node.
So, as root, I had copied the whole user folder in /home/ from one to the other.
This had messed with all the chowns, giving the ownership of everything to root i think.
I thought it might be something like this, and tried to fix it, but I failed.
Success came when i deleted the account, recreated it, and copied only the public_html folder over. Now everything works great
