Are those 0 values for inventory or for impact assessment? If it's 0 values for impact assessment, the problem is likely with having an impact assessment method (e.g. ,TRACI) that isn't compatible with the system of flows generally used in the lcacommons (the federal elementary flows list).
Can you point to the specific data in lcacommons that you're trying to use?
Have you tried running a calculation on a single process?