Bukkit

What steps will reproduce the problem?
1.Install PermissionsBukkit
2.Create a custom config.yml
3.Start server

What is the expected output? What do you see instead?
Permissions should work as intended and ranks should be set properly

What version of the product are you using?
2.0 latest (current date is 4/10/13)

Do you have an error log of what happened?
There is no error log

Please provide any additional information below.
It is replaced on every /reload /permissions reload or server restart.
It does say my rank is [Regular] with its correct color code, but this is a default rank instead of Owner, with completely different color codes.
I do not have the same permissions, using creativegates requires a permission every rank has, but I cannot use them (note: ops do not automatically get this permission so I cannot use this vital plugin)

This is not due to other plugins as I tried starting the server with only permissionsbukkit and the same error occurs.