According to a poster on the Friends of Boston's Hidden Restaurants Facebook group page, the South Station location of Cheeseboy is gone, with a Facebook post from the place confirming that it has indeed shut down. It appears that the remaining locations of the eatery in Downtown Crossing, at the Natick Mall, and at the service areas in Darien (2) and Milford, CT are still in business.
Cheeseboy first opened at South Station in October of 2010, joining the original location in Milford; in addition to the South Station shop closing, the group of eateries has also closed a few other locations over the past few years as well, including in Braintree, the Prudential Center in Boston's Back Bay, Providence, and West Nyack, NY.
The website for Cheeseboy can be found at http://cheeseboy.com/
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[A related post from our sister site (Boston's Hidden Restaurants): List of Restaurant Closings and Openings in the Boston Area]