There is a mistake in the ImprovementDefs.xml. The biosphere Manipulator is tagged as a colony unique improvement, which it should not be (according to the text).
<Improvement>
<InternalName>BiosphereManipulator</InternalName>
<DisplayName>BiosphereManipulator_Name</DisplayName>
<ShortDescription>BiosphereManipulator_ShortDec</ShortDescription>
<Description>BiosphereManipulator_Dec</Description>
<Icon>BiosphereManipulator.png</Icon>
<BuildIcon>BiosphereManipulator_Build.png</BuildIcon>
<ListIcon>BiosphereManipulator_Icon.png</ListIcon>
<ImprovementType>Terraforming</ImprovementType>
<PlacementType>Terraforming</PlacementType>
<IsColonyUnique>true</IsColonyUnique>
<LandPercentageMin>0.35</LandPercentageMin>
<!-- Stats -->
...
</Improvement>
To fix it comment the IsColonyUnique tag out, or remove the entire line.
<!-- IsColonyUnique>true</IsColonyUnique -->
