It's difficult to say without seeing the actual code, but there are a number of variables to consider.
First, consider that base data is stored at Local Currency for the Entity, and that LC is effectively just a pointer to the currency; so if the entity has LC set to USD, working in Local Currency or USD is effectively the same thing.
Second, are the two scenarios identical, in terms of properties? I.e. same input view for adjustments, same rates, same input frequency, etc.?
Third, are you sure your rule is the only thing influencing the output? I would run the With Logging options to track down what actually happens.
