Odd. Only the currently-selected layer should be affected. What are you trying to do to this one layer?
I always make a copy of the original and make changes on the duplicate layer. I am trying to crop the duplicate. When cropping, it crops all the duplicate layers.....no matter how many i have.
I've never had a problem before today!
You should be using either the transform icon (5th icon from the upper right) or using methods like selecting and clearing/cutting when working with a layer. As far as I've known, cropping using the Crop command crops the entire image just like it does in desktop Photoshop.