PermissionEx working, but Prefix have just stopped.

Hi, I was forced to reinstall my servers OS, after putting everything back into it and updating bukkit to new RB build (wasn't running it before) Prefixes have stopped working. It is the same config/plugins, but it has stopped working.

I'm using HeroChat for prefixes, and this is only on 1060, is it possible the prefixes stopped working due to this or is it something else?

If it is that herochat is out of date can someone reccomend something that will work?