Lightroom :: Importing And Including The Subfolders Without Getting Question Marks?

i am trying to import a folder of vacation pictures. it has 5000 pictures and there are many subfolders. It imports them where i want but it gives me question marks on all the subfolders. And the subfolders are empty even though it tells me how many pictures are in the folder. I right clicked the question marked folders and point to where they are and it just says they are already there and do i want to merge the folders. In importing i told it to include the subfolders. I have tried this twice and each time the same results. Very frustrating to have to scroll through thousands of pictures.