A few months ago, the IST gang mentioned that they were working on a utility called "Litter Box" which would help you clean up the odd files in a downloaded dropbox folder.
Apparently a version of LitterBox is now available and basic instructions exists at the Tutnitin Dropbox Help pages http://tlt.its.psu.edu/turnitin/DropBoxes.html
Download information and contact for that application is also available there. If anyone has any additional information, please let us know.