I guess that the problem is the World Standard Mapping setting - in Ecosystem material and/or in the for the Ecosystem used material. I did a little test and got a similar result as you described it. This should be set to Object Standard or Object Parametric. You don't have to edit your object loaded into the Ecosystem, you simply can edit the material used there. The second part of my screenshots show this.

One day your ship comes in - but you're at the airport.