I apologize that you are not having an ideal experience printing so far. I'd be happy to help with this.
This could be caused by a variety of factors, I think we will need some more information to narrow it down.
So I can best assist, I would like to take a look at your Canvas project. You can share it with me by following the instructions at mm3d.co/canvas-sharing. Please select all boxes to share printer, style and material settings. You can then send the link to me at firstname.lastname@example.org.
Thank you for your patience and sorry for the inconvenience. I look forward to hearing from you.
Sorry for the broken link, thank you for sharing that project! There are a few things jumping out at me here that I would like to adjust.
I notice you are using side transitions on this print. As the misallignment begins at a color change, I'm wondering if we are having some skipping during that movement that leads the printer to move off course when returning to print the rails. As layer shifting is much easier to track when we have a transition tower, I would recommend disabling side transitions and attempting a print with the tower enabled.
I would also recommend you enable supports, as there are overhangs under the rails that could use them.
You mentioned that you made the model in question. It may be worth running it through an .stl repair tool, just in case. Also, I was wondering what method you used for the successful version of the print at the top of your post? Were the components printed seperately and glued together in that version or did you use a different MMU?
Please let me know how it goes with these changes. If you have any questions in the meantime don't hesitate to reach out!