If the barrel alignment isn't OK you may experience op rod binding. If this isn't the case there is a possibility that the flash hider may be mis-aligned. There is a bit of allowance for lateral movement of the front sight to achieve a zero with the rear sight base set at mechanical zero (center index line on the receiver aligned with index line on rear sight base). I like to adjust for windage with the front sight first, keeping the rear sight base at the center position so that there is plenty of windage adjustment left in the rear sight for shooting at longer ranges. If at the end of the day your rifle is functioning properly and you can achieve proper zero by having the rear sight a bit off center, then there really isn't a big problem.... unless you are shooting at very long ranges and run a risk of running out of windage adjustments using the rear sight.
Are you using the original Norinco rear sight components? They are "soft" in relation to US or Italian GI components. That's why a lot of people opt to use the US/Italian made Garand rear sight components.