Hi,
I recently installed Vault onto my server and it unloads Chat Manager from the PermissionsEx Package. Why is this and is there a way to make it work?

Vault doesn't interact with Chatmanager. Vault hooks into the base PEX package for permission and info node (aka "chat") support. Also, Vault doesn't unload anything. It's difficult to even see what you're talking about without any logs.

I will reply wih the log the next time I start up the server. All I can say now is it unloads only when I start it up. I am running the latest version of Tekkit.

Sounds like an issue with ChatManager and Tekkit. Please report to PEX.