+ AA6YQ comments below
Executive summary - don't use the same virtual serial ports for CW Skimmer and Commander
More detail on SDR Console and Commander. In SDR Console you can choose both CW Skimmer and External Radio. If you set a virtual port pair in CW Skimmer by clicking on it, you must disable it or set another port pair for the External Radio. After you have the External Radio window open, you click on the question mark in the upper right hand corner of the window to bring up External Radio Options. You can then click on the "Omni-Rig" button to set External Radio ports in OMni-Rig. Finally choose the complementary virtual serial port in Commander and set the radio to Kenwood. If all goes well Commander will display "[Kenwood TS-2000]" in the top window bar.
+ Typically, one connects Commander's "Primary CAT Port" to a transceiver, and connects Commander's "Secondary CAT Port" to a panadaptor like SDR Console. How is the transceiver connected in your topology, Bob?