Non-PDF files cannot be processed and, evidently, do not have an output folder for “processed” files. They will simply be moved from the input folder to the output folder for non-PDF files. These folders can contain any file, for example:
Enfocus PitStop Server will also generate a report (“error log”) about this event. This report will be placed in a “Non-PDF Error Log” folder.
You could e.g. drop all files from your customer in the input folder, and then investigate what appears in the non-PDF folder for manual processing (images, PostScript files, Word documents, ...).