I have many counters. One is a PIC based 50mhz counter like this.
My PIC counter counts 50,000,00? (10 times a second). It also counts 50,000,000 once a second.
Assume the XTAL is accurate.
The PIC turns on the counter and 1 second later turns it off. The on/off is very accurate. The instruction rate is not important. At 1 instruction per micro second you simply do 1,000,000 instructions to get 1 second. If you were doing 100,000 instructions/second then do 100,000 instructions. The time a instruction is done to when the on/off happens is very predictable. Because the counter counts at 60mhz I have reason to believe the counter can be turned on/off very predictably with in 10nS.