The problem can be duplicated by selecting a group of files (zips, rars, nfo and diz) and queue them for "Download to Folder by Subject"
With v6.41 B4, it creates two folders.
1st folder, containing the proper files and subject
2nd folder with file_id.diz added to the 1st folders name and contains just 2 files - file_id.diz and descript.ion
With 6.40 Final, queued the same group of files, everything goes into one folder as it should.
A bug?