Eroyd,
Good observation. Yes, parallax will have an affect on point of impact. If your scope is set improperly, the cross hairs can drift as much as several inches at 100 yds, so will your groups if your eye position changes. Next time you go to the range, try the experiment in my previous post. Set your AO ring to 100 yds and see if it is really calibrated. If you have a range finder, try sighting at different distances. What you are looking for is cross hair drift, not actual focus. I tested several scopes and found the distance marks were fairly close to proper parallax correction. On some scopes, the focus was slightly off when the parallax was properly adjusted. My Leupold Vari-X 3, 4.5X14 50mm, seemed to track best and maintained proper focus at 100-500 yds. A BSA Contender 3-12X 50mm was the worst. The marks were way off and the focus didn't track well. I have a Burris Full Field 2, 3.5-10X, 50mm that doesn't have an AO. It's about 2 " off at 75 yds, 1" at 100 yds, dead on at 150 yds, and 1" off at 200 yds.
Lee D, Focusing "with your eye" may satisfy target clarity but has little to do with parallax. Again, try the experiment above. Adjust for best focus then see if you get cross hair drift.
Gunnut, On some scopes, the parallax adjustment has a definate affect on focus. I think they move different lens elements. For sure more noticable on cheaper glass. It takes some pretty good optics to make the retical focus and optical focus track properly.