Programs are timing out too quickly

Students are working specifically on Lesson 8, which requires user interaction, but some of their programs are ending too soon due to the timer. How can we kill the timer or pause it indefinitely?
Specifically: At one point, the program asks the user to press up for “yes” or down for “no” but the program ends before the user can answer that part.

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I’d like to know the answer to this as well!