Hi Michael, this problem you are experiencing could be related to two extra options that affects which layers/frames are modified when you apply an effect:
- The “Selected” / “All” button: Replace Color: Where is the "Apply to all frames in the active layer" button? - #3 by dacap
- The selected range of cels/frames/layers in the timeline: If you select a layer, a frame, or several cels, the effect (hue/saturation) will be applied to the all cels in the layer or frame (or multiple selected cels) respectively.