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That is probably because you are selecting the COPY option at the top of the import dialog window when you should be selecting the ADD option.
COPY copies images from one location to another and import them.
ADD just adds the images to the LR catalog from where they are currently located.
Then there is also the option to "Make Second Copy To:" on the right hand side of the import dialog but that option is only available with either the COPY, MOVE or COPY as DNG options. You need the ADD option to just add the images to the LR catalog file from where they are already located on your external drive.
You are correct. COPY images is my default setting during import. I never noticed the option.
This will save me time and much annoyance. Thanks for the help!
The problem you now face is getting the images on your external drive that you already imported using the COPY option to show as imported into LR. As it is now the images that are imported are the Copies of those files located in your Pictures folder.