Called in and it's just a PNR ordering issue. Would not have affected actual flight coupons when it came to flying them. (so they say).

Agent fixed it on my record and everything shows up ok.

Now... allow me to whine that in the process of fixing this, I somehow got re-deducted for the RPU that I'd applied to this itinerary. So now I have to get my regional back. *sigh* It's like whack-a-mole with these issues this week.