Turns out this was due to a difference between the ecoinvent impact assessment method and the one from openLCA, which I guess I should have thought of. For example in the ecoinvent version of CML 2001 only "carbon dioxide, fossil" and "carbon dioxide, from soil and biomass" seems the be included. The open LCA version also includes "carbon dioxide", "carbon dioxide, biogenic", "carbon dioxide, land transformation" and "carbon dioxide, in air".
Mystery solved