A file may require permissions to access other documents in Windows. It could be an XFDF data file that uses a PDF template located either in its own folder or another path on a network. The file would need permissions to access that file if the file or the folder that its located in has security to restrict access to it.
The best way to inherit permissions from a folder is to copy the file from the desktop or a folder on the system into the destination folder. All of the permissions in the folder will be inherited by the file. If you copy the file across the network into the folder, permissions will not be inherited and you will have to manually set them yourself.