Have you configured auto import to know about the new folder?
What do you see in the import status window when you run auto import? Is is recognizing the files?
You do have 'move processed files to' enabled, don't you? (
Tutorial - Preventing Duplicates).
Duplicates are rejected - they are not imported, so won't cause any problems other than delaying new imports (as described in the tutorial).
Manual Import does not move the files it reads as this will often be from an archive. (so I guess you do have 'move processed files to' enabled...)
If you can't get auto import to work please
report your problem and we'll investigate.