Special Stage timer trouble

When creating new Special Stages, I find that using the Countdown variable I can correctly adjust the amount of time one has to complete the stage, but I can't make the timer correspond to the changed amount of time. The timer at the bottom of the screen tells me I have more/less time left than I actually do. How do I synchronize the on-screen timer with the Countdown variable?

The Countdown variable is different from the special stage timer. The special stage timer is defined by using a control sector.