Sorry, Renaud, I guess I didn't read your post close enough the other day to realize that you're talking about two different signals.
After looking at the DAQ-STC VIs, it looks like the only way to accomplish this is with the following. The DAQ-STC updates its count with a rising edge on the source pin, and writes that count value to the counter buffer when an edge on the gate occurs.
Therefore, you'll have to use 2 counters, and since you can't simultaneously start 2 counters with a trigger signal, you'll have to use your own oscillator/timer signal on the source pins of both counters. Then, after both gates have been triggered, get the count values, get the difference, and then you can calculate the time between both.
It seems to me that this will
be the only way.
Mark