+ AA6YQ comments below
I wouldn't hold my breath waiting for a successful fix for this. It has been around since the beginning with the K3, over 10 years ago now. Elecraft did make firmware changes several years ago to address the situation, but perhaps their efforts may have been only partially successful. It looks as if there may be some kind of race condition in the radio's firmware that causes it to get confused about the TX/RX status of the radio if a PTT command via the rear panel PTT jack arrives while a CAT command to switch PTT is already being processed, and/or vice versa.
There is a simple workaround that applies regardless of which radio control software you are using: don't use two methods of PTT control in parallel. If you are using PTT via CAT command, don't connect anything to the transceiver's PTT input. Conversely, if you are using a hardware PTT signal, e.g. from a SignaLink, don't enable PTT via CAT command in your software.
Incidentally, instead of disabling PTT via CAT in Commander, could you not also achieve the same result by configuring WinWarbler's Configuration window, PTT tab, PTT Mode pane to select None instead of Xcvr Ctrl App? This may be a distinction without a difference...
+ The approach you suggest as the benefit of preventing requests from WinWarbler that Commander will ignore. However, the approach you suggest prevents only WinWarbler from directing Commander to issue RX/TX CAT commands. One could implement both approaches and have the best of both worlds...