Receipt Entry Indirect Costs

Hello,
We have a Receipt with 2 lines. Line 1 has a supplier price while line 2 is a free of charge item (0 supplier price). We have added an indirect cost with the disburse method being ‘value’. On the Landed Costs sheet we have selected “Value” as the disburse method as well. However, when we “Disburse Indirect Cost”, for some reason it apportions the charges on both lines. We cannot figure out what is going wrong as the environment has more than 10 companies but this is only happening in one company. We have checked most settings, including Company/Site Config but cannot find anything. Any pointers will much be appreciated.