Bukkit

What steps will reproduce the problem?
1. modding the config.yml file to certain needs
2. saving changes & starting server.
3. ClearLag folder ends up with a newly created fole called OLDconfig.yml containing the Custom fields that I wrote in.
4. Default Config.yml is put back into the folder

What is the expected output? What do you see instead?
Despite numerous suggestions on writing the config in; everything is completely ignored and the Plugin overrides the custom config.yml file with it's default source:

What version of the product are you using?
ClearLag v2.6.0

Do you have an error log of what happened?
No error log.

Please provide any additional information below.
Is it possible to edit the jar it self to fix this issue? Any code instruction would be appreciated. There is quite a few users that still use 1.6.4 for use with certain mods.
? The configuration of the server uses Cauldron the latest version of 1.6.4 usage.

I was able to forcefully get the config to function up to 90%.. as to work with only with Vanilla.

Is there a way to config this to work with extensions From Mods?