Microsoft has a long history of very poorly chosen names. There are at least 3 other Microsoft Stores -- their chain of retail stores (ala Apple Store), the online version of those stores, their multiple "Microsoft Stores" on the corporate campus that sell Microsoft hardware/software/books/swag to both visitors and employees predating the retail locations, and their employee-only online store.

I remember working with IIS at one point, and an object had a name like "site" then inside of the configuration files you had other "sites" that configured your site.

Finding errors for one was incredibly difficult because the other one kept popping up.

Sql Server and MVC also come to mind as less-than-ideal names.

.net, anyone?