Hi,
Not 100% sure what you mean but I think you're forgetting to reload the timer inside the ISR.

If you preset the timer to 12345 at the beginning of the program you'll interrupt after 65536-12345 cycles - the first time only. Then the timer will be free running and you'll get an interrupt every 65536th cycle (1:1 prescaler).

Or is that not at all what you're asking about?

/Henrik.

EDIT: Oh, well the man himself beat me to it - again.... ;-)