I know that Voice Attack and HCS both recently released upgraded versions of their respective softwares. It may be you have downloaded and installed the new HCS voice pack without first having upgraded the VoiceAttack application. When that happens, certain features of the newer version of the HCS voice pack, developed for the newer version of the Voice Attack software might not work. Also, make sure that Voice Attack is running before starting Elite Dangerous.
PS: Have you tried the "Import My Control Settings" command?
The latest patch for Verity threw the same error message up that it was created with a newer version of VA. Which I have already installed. So I took a stab in the dark and installed the latest beta version and the error message dissapeared.
Make sure that you also check that a VA plugin update wasnt included, of it has you also need to update that.
Other than that check your bindings in ED match with that of the VA Profile, import the bindings as mentioned above.
One extra tip.
If creating custom commands (i have a whole bunch i use to control the galaxy map, camera and VLC player, create them in a new profile that way if you update the HCS pack its easy to simply import the custom commands again should anything go wrong