This likely has something to do with the direction of the relationship you created in PowerPivot.
Can you confirm the direction of the relationship (i.e. which table in your relationship is listed as the Lookup Table)?
Also providing a sample of your data, or at the very least the field names from each table, will also help you get a quicker solution to your problem. Additionally, what measure/measures are you using in your flattened pivot?
It sounds to me like your Branches table should be the lookup table, but the result you are seeing seems to indicate the customer is the lookup table currently.
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