Im using an i9300 and I've only had an issue with root on the very first build and since then no issues. I did a fresh install of last weeks build and all was fine.
When doing a fresh install what I do is jump into LBE Guard and make sure root is enabled. From there I then launch the app that requires root and you will see the popup asking you if you want to allow root. All you do is allow it and off you go...
Then using the MIUI Backup app I just backup the Permission Manager settings and then I don't have to worry about it bugging me when I do another fresh install
Sometimes I've experienced that the app doesn't have root immediately but by either killing the process or rebooting the phone this resolves it.