I am also having this issue with CityEngine. My terrain layer does not align with my roads or building layers despite them aligning in Arcmap. I have made sure that all layers are in the same coordinate system (NZTM). I have made sure that they are the same extent. I have tried using Shapefiles to see if that would help.
I have inserted a screenshot of the issue, with the red arrows indicating the difference.
I'm a bit stumped as to what to try next. If someone could give me some suggestions, it would be greatly appreciated.
After tweaking some more I worked out that the Aerial photo was the cause. It wasn't quite the same extent and I re did it completely which resulted in it working. Thanks anyway