I've been running into this problem alot in the last 6 months and I'm finally fed up. Basically, at some point while working on my CS3 projects, something unknown to me happens and I can no longer change a layers parent with the drop down box, same thing goes for layer control drop down boxes in the effects panel. Now, I can still change a layers parent with the pick whip, which is why I've just lived with the issue. But I've now run into a problem where I'm using a Layer Control expression effect and I cannot change the layer at all there. I click it and nothing happens, no response at all. Any help here would be greatly appreciated.
Please be more specific. Provide info about the number of layers per comp, comp settings, what items are referenced/ used using the layer controls etc.. Also provide screenshots (use the camera icon to attach)/ info about the structure of the project or the project itself. I've never encountered such issues myself, but it is imaginable that too many references/ too many layers create some sort of overflow that prevents the list from being drawn or populated correctly.