Yes, it is the net time. The way you are using the S4 (I'm guessing), that is the net time from sync.
If your computer crashes during a race, you can continue by using this net time in the Program 3 TOD program by doing the following:
Put the toggle switch to the C position and clear the time by pressing the yellow and red together. The clock clears to all zeros. (but the A switch stays in TOD sync) Send the racer and upon the finish you can use the N time under the TOD impulse for finish net time.
Repeat the clearing by pushing the yellow and red together again and send the next racer.
When your software comes back around you can manually put the times back into the system. It also helps to scribble the bib number next to the TOD and N times to keep track.