I have just setup a new custom theme with little/no data and yet Wordpress has made an update notice about upgrading it to "1.0.1" and I cannot for the life of my work out why.
I have stripped down the theme to the following files:
I have a blank index.php and style.css:
/* Theme Name: Fresh Description: A customisable theme built just for your website Version: 1.0 Tags: white, two-columns, fixed-width, custom-header, custom-background */
An obvious fix is just to increase the version number, but it is concerning that for some reason it is checking an external source for version updates when it is not supposed to. I have a large amount of themes in my themes directory, some of them start with the word "fresh" but none are actually called just "fresh".
Edit It appears to be loading the data for another theme called "Fresh" on some wp-themes.com, I have renamed my theme and it's still checking. Maybe some sort of transient cache isn't clearing?