Jimmy,

If you use the sight-tube to achieve good collimation and good secondary alignment then using the autocollimator and the cheshire should only "fine" tune collimation with small adjustment. It is not clear to mewhy you are dramatically adjusting your secondary mirror after collimating your scope with the sight-tube – this should not be the case.

Your photo suggests a tilt/rotate error. To fix it, you will have to rotate your mirror in such a way to move the top secondary mirror edge as shown in your photo closer to you and the bottom secondary mirror edge away from you. The amount of rotate has to be SMALL -- just a touch. Then only use the secondary mirror adjust setscrews to stack the autocollimator reflections. Do not forget to check your final setup with a cheshire. If it is off, then iterate between the cheshire (by only adjusting the primary mirror) and the autocollimator (by only adjusting the secondary mirror) until both tools show good collimation.
Do you have the XL or XLK version of the autocollimator?

Jason