You can not start 2 VIs simultaneously, I would say the usual difference is ~ 1ms (good programming), but can reach several ms in worst case. If your pulse rate is 10 Hz, then failure chance is ~2%.
You need some kind of hardware synchronization:
1) daqmx route. set both tasks source terminal to PFIx (not input terminal PFIy). Use daqmx routing palette, disconnect terminals PFIx and PFIy, start both tasks - they will wait for the input pulse. Connect terminals, both tasks will start with the first pulse that arrives.
2) Use one more counter (single pulse generation task) as an arm trigger source for both tasks. Start tasks, they will not run untill receive arm pulse, then run that additional task.