17.7.2 Prescaler Reset
The prescaler is free running, i.e., operates independently of the Clock Select logic of the Timer/Counter, and it is shared by Timer/Counter 0 (T0). Since the prescaler is not affected by the Timer/Counter’s clock select, the state of the prescaler will have implications for situations where a prescaled clock is used. One example of prescaling artifacts occurs when the timer is enabled and clocked by the prescaler (TCCR0B.CS0[2:0] = 2, 3, 4, or 5). The number of system clock cycles from when the timer is enabled to the first count occurs can be from 1 to N+1 system clock cycles, where N equals the prescaler divisor (8, 64, 256, or 1024).
It is possible to use the prescaler reset for synchronizing the Timer/Counter to program execution. However, care must be taken if the other Timer/Counter that shares the same prescaler also uses prescaling. A prescaler reset will affect the prescaler period for all Timer/Counters it is connected to.