...perhaps Kirk's "tinkering" with the Kobayshi Maru programming was not discovered until (years?) later, and as punishment Starfleet is requiring Lt. Cmdr. Kirk to take that course again at the Academy (maybe the Kobayashi Maru test is the final for an Academy Course).
They find out he cheated on the final and make him retake the whole class.
Although in my scenerio, does he beat the test the second time, also? And if so, how?