This is caused by a Windows hardlink point amongst your instance's config files. Cortex's game packages don't contain config files, rather letting Cortex itself create the config file, so the only way this can happen is when someone places a config file in the game's engine directory. We highly recommend against running game servers right out of the engine directory for this very reason. Here's how to clean it up:

• Log into Cortex and stop every running instance of that engine type.
• Log into your server, open the Windows Explorer, and delete the config files from your engine and instance directories.
• In Cortex click the Edit Config link for every instance and resave their configs.
• Restart your instances.

That should clear things up for you.