Color replacement tool won't work at all

Hi, I am using photoshop CS3 in 10.6.2. The color replacement tool is not a tool I have much experience with, but am wondering why it won't work at all. I have reset the tool to its default preferences and tried using it on multiple documents and with different users and it just won't work. Nothing happens at all. I have watched some tutorials on using the tool and it looks easy enough and quite straight forward to use. I have tried every setting for the tool and still nothing happens. I am working on the top layer and have not selected anything. I have tried merging all the layers onto one layer incase the tool wasn't working because it would only replace the color of what is on a layer.
Thanks for your help.

The mode is color. The sampling is continuous and the limits are contiguous. These are the default settings for the tool.
I am noticing that the tool does work a little. I created a new document with 3 layers. The bottom layer is a white background. The middle layer has a blue square on it and the top layer is blank.
I notice that the color replacement tool won't work on the white background layer or the top blank layer, but only works on the middle layer. Does the tool only work on the same layer that has a color you are trying to replace?
When I hit the command option shift E keys to merge the layers into a copy, the tool only worked on the part of that layer that had the rectangle drawn on it and ignored the white part of the image.

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