I'm just guessing but it sounds like you duplicated the comps in the layer stack instead of the project panel, which doesn't really create a new comp, it just creates an "instance" of the existing comp.
To actually creat a new independent comp you need to duplicate it in the project panel and then add that new comp to the layer stack. Then you can change each independently. There's also script called True Comp Duplicator (or something) that will also duplicate all the compositions dependencies like files and assets.
Remember that your comps and files actually exist in the project panel, not the layer panel. If there is one file (or comp) in the project panel then any changes you make to it will show up in every instance of the file or composition in the layer panel.
Hope that wasn't worded "confusingly" :O)
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