I have v6 standalone. I'm guessing you accidentally ticked the box labelled 'Into Subfolder' in the Destination panel of the Import screen. The Destination panel is the lowest right panel (it may be closed by default). The very first item in the panel is a checkbox that says 'Into Subfolder'. Is that ticked? If it is, try unticking it then import something to see if that has cleared up the issue.
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