I am not a rly person. But I can guess (may be wrong). The wait list confirmation occurs in two priority
1) According to the WL sl number i.e. according to the date and time of issue of tkt regardless GN and or CK
2) According to the road side quota (such if some one has WL from HWH-DHN and there is vacancy for this section then the first person having WL for this section gets the seat)