When I use an Autonumber with single-page files, only the page number is shown in the filename and not the Autonumber.

This happens when the autonumber is in the same format as file page numbers. By default, page numbers have 4 digits–0001, 0002, etc. If you need to use an autonumber with 4 digits, you should set the FILE_NUMBER_LENGTH setting in the INI file to 5 (accessed from the Advanced tab).