I have been modeling the alignment procedure and have arrived at several conclusions.
1. Irregularities can occur in go-to based upon errors in your Dec home position. Similarly errors in cone angle will persist even after three star alignments. Thus you need to assure these are minimized before you perform the alignment. I note the cone angle is correctly compensated for in the three stars used in the alignment but not across the sky.
2. Your precision of centering during the alignment can affect your result. So use a cross hair eyepiece and get close during alignment.
3. When you sync on an object you bake in the Az El rotational error imposed by home error and measurement error. These errors get rotated around the sky and affect other objects.
4. The residual errors discussed above affect some objects more than others depending upon where they are in the celestrial sphere. Thus you can have good results in one object and poor in another.
My simulations suggest that the cone error and Dec home.error are to blame for the things you are seeing. It suggests you have Dec home error likely on the order of 1 or 2 degrees. You can eliminate Dec home error using the procedure I posted in the mounts subgroup in the files section. Do this before you start after you have.set up and leveled the mount . It only takes a a few minutes. As for cone error you should eliminate it using the method posted by Jerry with a link to the Astronomy Shed YouTube channel.
I don't believe there is anything incorrect with the planet vs DSO pointing. While possible, the results you are seeing are far more likely due to one or both of Dec home or cone angle.
Wes, Southport NC
PMC-8, ES ED 127, 10" LX200GPS, Astro-Tech 8" Newt, ETX-90
Polemaster, Orion ST-80 and SAG
Electrical Engineer, Retired