[Only slight spoilers ahead, nothing you can't figure out from the theatrical trailer.]
In Tron Legacy, Kevin Flynn disappears in 1989, leaving his entire life to fall apart without him. This includes his company, the raising of his son, and his arcade, Flynn’s, which is shown in the film having been closed down and all the game machines covered in plastic. When Kevin’s son, Sam Flynn discovers the arcade and turns the power back on, all the machines come back to life. . . including an original Mortal Kombat arcade machine, which didn’t come out until 1992.
Given Kevin Flynn’s hidden office isn’t discovered until 20 years later, it’s fair to assume that the arcade was shut down as soon as he disappeared. If the arcade had stayed open without Flynn around, his employees would surely have found the office behind the Tron arcade machine just as easily as Sam did.
Continuity mistakes for the win! And that concludes my obligatory uber-nerdery for the year. . . everything from this point on will be completely voluntary.