Hello!
For some reason, even non-multisite wordpress cloning is not happening properly. I notice, the site which gets cloned has it's 'siteurl' and 'home' values changed to the values of the new cloned website. The cloned website, works perfectly though.
So, if I'm cloning dev.example.com to dev2.example.com, the mysql values (siteurl and home under wp_options) for dev.exmaple.com get altered to the values meant for dev2.example.com ie. 'dev2.example.com'
This is happening after the 1.13.1 update, and it would be excellent if someone can confirm this as well.