I just ran a test with multiple windows open for the same file and got the same result you did. I did some further testing and I'm pretty sure this is what is going on:
FileMaker ignores the found set(s) you have in other windows and imports the found set that happens to be open in the window you are working from, even though on a layout that is currently inactive.
This makes sense, if you think about it. You can have two or three windows open, each showing a different found set (although one of them is hidden because you are working from a different layout/table). When you run the import process manually there is nothing to tell FM which found set you want to import, so it defaults to the one in the active window.
In your script, you will need to include a script to navigate to the window that holds the set you want to import, which will overide this default behaviour.
Thanks, yours were indeed Key Words - your explanation is consistent with what I'm seeing and makes sense. Now that you've clarified that this behaviour is, in fact, reproducible, I can handle it in my scripts. Appreciate your help.