Hi folks,
I think that PHP 5.3 is quite an old version, therefore most of mine and I'd assume others' deployments are using v5.5 in which mysql_* functions are deprecated and unsafe(!) so it should be replaced with PDO.
From what I've seen (I haven't seen all of the code) most code uses mysql_* functions.
I think this is a massive issue, which should be taken into consideration for the next update. I will try to find some time myself to contribute and rewrite it, but obviously it's a community driven project so if anyone has started doing it, I'd like to give a hand.
P.S. Main attraction of Zpanel for me, was the aesthetic design (better than most paid products). Most of other platforms look like crap, so well done guys. Love the UI and the functionality. I'll try to contribute as much as I can.