Leaving the game paused won't cause that kind of problem. Your computer's system clock can be changed in a lot of different ways, sometimes unintentionally. The clock can be inadvertently changed if you double-click that little Windows clock in the bottom right corner to check dates and times (a lot of people do that without realizing that it changes anything on their computer). Also, Windows has the ability to set the computer's clock using an Internet time reference, so if the clock was inaccurate the resulting time correction could affect the game.