Well, if you define things more precisely you’re more likely to get answers
First, don’t confuse MODx documents with the filesystem of your server : creating a physical folder with a same name as a MODx document is not a good idea especially if you use clean URLs
Are you using the FileDownload snippet (with or without the FileDownload plugin) ?
If so what is the snippet call ?
If not, please give this a look this will save you a lot of trouble, you seem to have strayed in the wrong direction here (unless I am mistaken, which of course can happen)...