Can you at least post drawings of your automated setup and describe it a bit more in depth? It is hard to understand the issue, if we cannot see what your setup is.
For instance, if you are using some form of markers, are you leaving the markers as they are and then simply flipping the side of the object? If so, that would explain the alignment stacking those on top of each other, as RC alighns the images according to the markers that haven’t moved. That ore something like that could be the issue here.
But then again, it could be something completely different. We would need more information.
Cheers
Guillaume