The queue manager will leave a file in the incoming queue when: 1) Some "security" software does not allow the cleanup daemon to write to the qmgr FIFO. Try without SeLinux, AppArmor, etc.
2) The queue file system is not on a local disk, and either file server's clock and the Postfix machine's clock are out of whack. 3) Mailscanner or other non-Postfix software directly manipulates Postfix queue files. 4) The file system does weird things with the "execute" file permission bit. Postfix sets this bit when a queue file is ready for delivery. 5) The queue manager is blocked for other reasons. Some vendors make changes to Postfix source code and thereby break things. To investigate, does the delay happen with local submission (the Postfix sendmail command)? You wrote that you made the queue manager verbose, but there is no verbose queue manager logging in your report. Wietse