Bukkit

What steps will reproduce the problem?
1.having prefixes setup for say an admin
2. Typing /yapp
3.all the prefixes are removed

What is the expected output? What do you see instead?
Pulling up the command prompt. The command prompt is pulled up but all of the prefixes are removed

What version of the product are you using?
Most current

Do you have an error log of what happened?
No

Please provide any additional information below.
The prefixes return when there is a server restart

If the prefixes return during a server restart then just reload the server every time you modify something. I'm pretty sure yapp comes with a plugin save/reload to do that if you don't want all your plugins reloading.