Rounding in Perfect Dark
Rounding is the phenomenon which occurs in Perfect Dark when the last time displayed on the on-screen game timer is a second faster than the time which eventually comes up on the end screen.
For example: you finish a level and the last frame shows 0:55.97. Perfect Dark usually rounds times downwards to the nearest whole second meaning this should earn you a time of 0:55. But the game gives you a time of 0:56.
Why rounding occurs
Rounding occurs simply because the timer keeps running after the last frame. The in-game timer does not update itself once every frame, it updates once every hundredth of a second, whether there's a new frame going up on the screen this instant or not. After the last frame, depending on the frame rate (which in turn depends on how many other in-game characters are around, how many explosions are nearby, whether anybody is saying anything at the time, and so on), as much as a tenth of a second can pass in which no frame loads but the timer keeps running.
In addition, even though conditions may be optimal at the end of the level (you're looking at the floor, there's nobody nearby, e.g. Carrington Institute: Defense), the game ALWAYS spends a brief moment not updating the screen, but still counting time, while simultaneously quietly loading the outro cinematic sequence. This is a fixed period of time (which varies by level, however) which cannot be reduced, and also adds to the size of the potential rounding error.
Make no mistake: the game didn't cheat you out of a second. You ran 0:56. The SCREEN cheated you out of knowing it. It's all, ultimately, technology's fault.