First, with regards to your weird issues. Are you using DMX cables and also what are you using for a controller?
As for realignment after each setup, this is common. There is no exact way to setup 100% the same each time. A few fractions of a inch can be huge depending on target, angle, and throw distance. Also, the with a change in venue comes other changes, like trim height, stage size, etc. For shows I tour with, I have to update my positions at each location.
The DJ Scan is only 8 bit pan and tilt. If you need more accuracy, look for a fixture with 16 bit pan and tilt. This increase the accuracy exponentially. AMDJ has 16 bit pan and tilt fixtures. I would recommend going to Elation if you needed more features, output, and a more road worthy fixture. You are going to pay for all that however vs AMDJ. So it seems like AMDJ is fine for your needs, you simply need to find a better AMDJ fixture. With the 16 bit though, expect to pay more money.