Most likely the fly is getting into a different zone without the indicator versus with it.

One thing with an indicator is that if your leader is supple enough to hang straight down from the indicator you have absolute control over the depth the fly fishes at provided you wait long enough for it to sink. It is much mor difficult to be certain of the depth without an indicator.

With the side by side comparisons with my angling friends if the non indicator rig is working better then it is usually because the indicator is set so that the fly fishes too deep. Sometimes it is the other way around.