There is a glitch. I blogged about it a while back. I had the same thing happen with an S fare. I wrote in weeks ago, no response, so I called yesterday and the rep opened up a ticket. She tried backing out the flight and re-crediting it first, and that didn't work. It was the first of this issue this rep had heard, so go ahead and call in to report it if it's also happening to you. It might move faster.
EDIT: Maybe not a glitch based on what Westcoaster posted below? The CSR I spoke to thought it was an issue and escalated it, so I'll update with whatever I hear back.
Last edited by PWMTrav; Feb 18, 2015 at 10:24 am