Bukkit

Describe to us the issue that you're having:
Hi,

I installed bPermissions after using PEX, which didn't work. I configured all of the files and such, including tracks and groups. I ran my server, and I noticed that it created another permissions.yml file in my server folder, not in the pluggins folder. I think that this is messing my server up. Also, in the console, it says that bPermissions is detected! Using bPermissions for permissions.
But it still doens't work. I hope you can fix this. Thanks.

Which steps will reproduce this problem?:
1) Run the server
2)Wait for it to be done loading server
3)The extra permissions.yml file is created!
....

Do you have an error log of what happened?
no

Which version of bPermissions are you using?: (Please don't say "latest"!!!)
v2.10.7c

Which version of CraftBukkit?: (Please don't say "latest"!!!)
it runs minecrfat 1.6.4

Which OS?
Windows XP

Any other information we may need (plugins, configs, etc):
Plugins I have installed
- World guard
-DisguiseCraft
-essentials
-bPermissions
-world edit

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Does this still occur on the latest version? 2.10.9