My rear end is square but I have more room on one side than the other. Sooo...dont adjust based on the quarter panels. ^^^^How are you making adjustments? I would also not be using the quarters but rather tram points n the frame, use the holes to see if your square.
A thrust alignment is what will make it go straight down the road. When you align something like the subframe an 1/8" is something to shoot for but a 1/4" is not that far off.