I also have a Kinesis Advantage, but I couldn't reproduce it. Have you tried resetting the settings by holding Prgrm+Shift+F10?
Does it also apply to holding other keys? Or have you tried swapping command with some other key in System Preferences and holding that other key and tab?
If it's a hardware issue that only applies to some keys, you might use KeyRemap4MacBook to map some other key to command. For example I have moved all modifier keys under the left thumb:
<autogen>__KeyToKey__ KeyCode::DELETE, KeyCode::SHIFT_L</autogen> <autogen>__KeyToKey__ KeyCode::FORWARD_DELETE, KeyCode::COMMAND_L</autogen> <autogen>__KeyToKey__ KeyCode::HOME, KeyCode::CONTROL_L</autogen> <autogen>__KeyToKey__ KeyCode::END, KeyCode::OPTION_L</autogen>