The scan_counter label is intended to be used as a sequential counter of acquisition progress, i.e., independent of specific sequence loop counters. That being said it has been used infrequently by users and filled out correctly even more infrequently. So it is being considered for deprecation in version 2.x. No decision has been made.
Either way, if you want to fill it in "correctly", it should be "0" for the first acquisition and then increment by 1 for every subsequent acquisition.
Hope this helps,
Michael