I am VERY new to shooting with a scope (only got my rifle on Friday) and during my research, somehting like the OP's experience was given as a good sighting method if you have a means to hold the rifle still. Aim centre. Shoot. WIHTOUT moving the rifle, realign the scope to the pellet hole, which should account for the drift or aligment diffence.
Any comments before I see if this works for myself?
Regards
Mark
Some air, some section 2 and a growing collection of section 1. Boy, this FAC stuff is addictive!