The easiest way to explain or why I suggested the things I did is since I'm rooted, before trying or flashing a new Rom I always start with a clean base. That way problems won't arise with the new rom.
I would always suggest wiping your phone (factory reset) before or after flashing a new os update.
Some updates can be incremental updates meaning they're bug fixes and these incremental updates wouldn't require a complete wipe but only wiping application cache and/or application data would probably suffice.
Since you've received an os update, going from 4.1 to 4.3, I would recommend a factory reset.
Again, results may vary for different people since not every phone or a phone's setup is the same.