In the configuration file there is the offset adjustment in "Timer2 0.00".. which must be set to zero then a SER must be carried out at 1000fps by reducing the format with SharpCap. You open your SER then you adjust the delay between the led/pps signal and your timestamp. see astrosurf link below.
http://www.astrosurf.com/topic/163700-ma-synchronisation-dun-pc-au-1pps-offline-pour-les-occultations/?tab=comments#comment-2338266
Saci