Is there any way of doing this through a batch or powershell script? I'm looking for a way to set up several new servers.
The only thing I found on the subject leads me to believe you cannot: from :http://technet.microsoft.com/en-us/library/cc785060.aspx
The message store location must only be modified using the Storage tab, in Computer Management, Services and Applications, Message Queuing properties.
Edit - I also found this article. It lists some registry values, but again advises against it http://blogs.msdn.com/b/johnbreakwell/archive/2009/02/09/changing-the-msmq-storage-location.aspx