I seem to remember reading somewhere that the alignment stars are deliberately placed a little out, and the slewing process to the star is a necessary part of the alignment process
Old wives tale
The scope uses dead reckoning to centre the first star.
It does a "synch" on that star, and thats why the second slew gets much closer. After the first star is centred, all the autoaligning generated info is discarded.
The three things that affect the first slew are
a) base level
b) north setting of OTA
c) level setting of OTA.
If you have a semi permanent spot where you set up
do a two star align then tell the scope to slew to AZ = 0, Alt = 0 ( via the Hbx )
Note the line the OTA makes as that is the "true Nth" for that spot.
closer to level an