Quite scary to jump in here without seeing actual data;) but I will give it a try.
I assume your "primary source" contains mastersdata (e.g. Costcenter, profitcenter or pointers etc) and transaction data (e.g. sales ect). This is the "left-side" of your join. All other sources contain masterdata (attributes of.....). Now you should ensure yourself that all sources are connected with the right dimensions "under the key" of each datasource. Is it possible to share your workbook it will really speed up the solution time. There are ton's of girls and boys who love to help out here on the block:)
Thanks Norbert, I examined my data sources and discovered that some of my lookup tables in the file I was given contained duplicate values in them so data was being counted twice in certain scenarios, once I corrected for this then the data was as I expected in the system.
Glad you were able to make it happen!