i have the same issue for a flight on March 23. I have been waitlisted since booking when I used a regional for upgrade. Yesterday and still today RN9 is listed but no upgrades seem to be going anywhere - certainly not to me. I called 1K desk she acknowledged that there was upgrade space available but she could not upgrade me manually. Said to wait for the system to work automatically. 24 hours later, still no joy and fare code still showing RN9
I just had one of these. Had waitlisted my brother for an upgrade with an RPU. I noticed this morning that the flight had gone R1 but he was still not cleared. Called and the agent said they had been told that sweeps did this and they couldn't intervene. I told her that was wrong since if I was applying the upgrade right this instant it would clear immediately so how could an existing waitlist not. So I had her remove the upgrade request from the record and then reapply it and, of course, it cleared immediately. This is ridiculous - and it's not about jumping queues. If anyone can come along and upgrade against R space instantly then there is no excuse for any uncleared upgrade to be pending against that space.
So - suggestion - if you find yourself in this situation have the agent remove the RPU (or GPU) and reapply it. Only problem is that you probably can't do this if it is a multileg upgrade where some leg has already cleared (not sure). It really is absurd that in 2012 you need people watching an automated system constantly to make it work. I have developed this silly habit of doing a morning scan of all the future reservations in my account for "events" - and I have 11 PNRs currently there. I never had this habit with the old systems.