One of the stations in Dallas that used to have the problem (WFAA) no longer has the problem. I sent an email to one of the engineering people at WFAA asking if they had made any recent changes to the encoder that might explain the difference, since that might be useful in approaching other stations about it, but they never responded.
In my experience, approaching a station with an issue like this is only worthwhile if you can explain exactly what's wrong. There are literally dozens of different settings the encoder has that might be triggering this, and without even a guess as to which one is the culprit, they aren't going to just go making changes and hoping something fixes it, especially since the encoder is the single most important piece of equipment at the station. Any change to that is being done with a specific plan of what's changing, why it's changing, how and when the change will be implemented, and how to restore it if things go wrong.
Reception, channel detection, network issues, CableCARD setup, etc.