I think that you have asked a great question. Something that many engineers may not be aware of is that the DAQ device itself does not actually create the time stamp. It is created by the comptuer system when the data is retreived from the DAQ card. Because of this, the time stamp is actually delayed by a significant amount. This delay may be less than the resolution for time stamps (one millisecond) but it can sometimes be greater than that. This Knowledge Base article discusses it this in more detail: http://ae.natinst.com/public.nsf/web/searchinternal/5d42ccb17a70a06686256dba007c5eea?OpenDocument
If your pulses are closely spaced, the generating a timestamp for each aquisition is not practical. But, if your pulses are spread apart by a significant amount (more than 0.1 seconds or so depending on the specifics) then the timestamp might be accurate enough to be practical. One way to do that with counters would be to use the Get Date/Time in Seconds VI in LabVIEW just after the DAQmx Read VI. Then, once the Counter Input measurement is complete, LabVIEW will create that timestamp very quickly afterward. Please notice that there will be some time delay between the completion of the read and the creation of the time stamp.
Jeremy P.
Applications Engineer
National Instruments