Took my AR to the range today.  The rifle had been sighted in according to the manual.  today I flipped the large apeture up and the rifle shot 3" left at 100yds.  Has anybody else had a windage problem when changing apetures?  The apeture apears to ride on a threaded rod.  should the large and small apetures be offset to prevent this problem? For what its worth the rifle is a homebuilt.  PWA Lower
Bushmaster lower parts kit
Armalite A2 upper
Bushmaster 14.5" heavy bbl with phantom
Armalite bolt carrier
Bushmaster Bolt
Win. Q3131A ammo
Any info would be appreciated.  Also, is there a range that I could zero in that would alow me to hit a 6" circle from muzzle to 300yds with out ranging with the rear sight?

Something is wrong. Maybe the sight was drilled incorrectly.  If that is the case Armalite ought to fix it.

Rear windage is 1/2" min clicks which would be a 1/2" at 100yds. The slight shift " less than 1/2min" when switching apertures is very insignificant.
If your having a 3" change it is probably due too poor sight picture ( sight alignment ) with the large aperture. Have someone else shoot it and see if it does it to them..

Quoted: today I flipped the large apeture up and the rifle shot 3" left at 100yds.  Has anybody else had a windage problem when changing apetures?

The spring and ball bearing inside the windage knob usually return the windage screw/aperature to their original positions, but sometimes the pressure exerted by the flat spring under the aperature prevents that from happening.

After flipping aperatures, be sure the windage screw is returned to it's original position.