The problem is when the counters are started or reset. However, even if you start the dividers at the same time the 'phase' will not be the same. The time shift will be the same. For example, if one frequency lags the other by 20ns then they will have the same time delay after dividing. But 20ns at the lower frequency is not the same phase shift as 20ns at the high frequency.
If the dividers are not simultaneously reset, even the time shift will be wrong.
Keith