Hi, that seems to be the problem. It looks like one point of the upgrade didn’t go through. You need to have all the entries with a blog_id of 1.
There is a bug in the code implementation of the metabox which is causing this issue. I’m working on a new version that should fix this and will upload this shortly.
You could try hitting the Clear Duplicates button which should delete out all the duplicate entries. However, as always, please backup your database before proceeding.
If you’re in a hurry, you should run the following query on your database:
ALTER TABLE wp_top_ten CHANGE blog_id blog_id BIGINT( 20 ) NOT NULL DEFAULT '1';
This will force a default value to the blog_id to be 1 and any future updates on the metabox would automatically set the blog_id to be 1 and update the count accordingly.