I have just setup a brand new WPMS v3.1.3 website. I installed New Blog Templates v1.2.5 and created a new template using Blog ID #1 (the main / home blog).
I created a new blog using the new template, but I am getting the following error in the sidebar when viewing the new blog: Warning: array_key_exists() [function.array-key-exists]: The second argument should be either an array or an object in /home/esempire/public_html/wp-includes/widgets.php on line 858
This new website is the most basic install possible. Everything is default and NO additional plugins or themes installed. Just WP v3.1.3, the default twenty ten theme, and your new blog templates plugin.
The install is located at: http://escortempire.biz/temp1/