Hello Zoltan,
I would suggest using the counter gates to synchronize the counters. You will need to externally run a wire from one of the DIO lines you're not using to one of the counters' gates. When the counter gate is high, the pulse train will be generated on each counter. Both counters will need to use the same PFI line as the gate.
There is an example program that ships with LabVIEW 7 called "Gen Dig Pulse Train-Continuous-Pause Trigger" for DAQmx. This demonstrates how to configure the counter to only generate the pulse train when the gate is high.
With this configuration, you could synchronize the counters by writing to the DIO line which is wired to one of the counter gates when you're ready to start the pulse train generation.
Hope t
his helps.
Kristi Hummel
Applications Engineer
National Instruments