I am afraid I need clarification. Here's how it's supposed to work: when I click in the "seconds" part of time box, two digits for seconds become selected. Then I type first digit, it replaces the selected digits so there's only one digit displayed in seconds box. Then I type second digit and it appears after the first digit.
At what point the behavior you see deviates from what I see?
Also, what's your Windows version? That may be a contributing factor.
Andrei