After having been free of these out-of-sync messages since May, they're now back. Had two within the past week solely for upgrades clearing.
On the first one, triggered solely when a return flight CPU cleared at 96 hrs., the SLC CSR told me that it was a good feature, not a bug, since it served to trigger calls from some customers who didn't want to be upgraded and others who wanted to know how to be assured that an upgrade attached.
I'm holding to my original view, that it's a costly bug, not a feature.