Do not be alarmed, this is an expected behavior for this report. The Ranking Areas – Standard Geography – Customers report only lists geographies that contain customers, so while the percent (%) column will always sum up to 100%, that will not necessarily be the case for the Base % column. The Base % column is factoring in all those geographies where no customers are present.
For example, if the Base % column sums to 44%, it can be inferred that ~56% of the households (in the Trade Area) are found in the component geographies where no customers are present.