Today I put on hold a domestic award with a stopover on the return. It had priced at twice the correct mileage. I called the PM line and the agent contacted the rates and reissue desk. According to the agent, the reissue desk is aware of the issue and confirmed that IT IS indeed a computer error and that they were not aware of a pending policy change. The agent was told to ticket the outbound trip and the first part of the return (the part from the inbound origin to the stopover city) and then have the reissue desk add the last part from the stopover city to the destination. I didn't actually go through with it, though, since the trip may not happen.
On a separate note, for testing purposes, I was able to correctly price a domestic award with an open jaw.
What remains to be seen, however, is whether we'll again be able to book both an open jaw AND a stopover in the same domestic award. The rules don't permit it, and with programming changes being made, that capability may disappear altogether.