Copying a Folder with Files into Vault Issue

I have PDF's that are separated into folders (say 5 folders with 5 files in each).  I can copy and paste these folders to a "PDF Holding" folder on the server.  I have a program that automatically moves the folders and files to vault.  The folders will add to the vault no problem, but the files in the folders are in .  I have added pdf to add files option in admin tool.  If I do just the PDF's and not the folders, the PDF's are added.  Has anyone come across this before?  Any Ideas as to what is going on??

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