Jimmy, centering/rounding the secondary mirror under the focuser is accomplished by the sight-tube -- not the autocollimator. Stacking reflections with the autocollimator is independent of the secondary mirror position under the focuser. Check the following animation. Each frame shows good axial alignment but for a different secondary mirror position. Also refer to the following link

Questions:
1- Do you stack the autocollimator reflections by only adjusting the secondary mirror?
2- Do you iterate between the autocollimator and the cheshire until both show good alignment?
3- Do you use CDP (explained in Catseye documentation and website)?
Jason